Synthetic beta-amyloid peptides capable of forming stable antigenic oligomers

ABSTRACT

Synthetic Aβ peptides, oligomers, their methods of synthesis, and their applications are provided. The Aβ peptides can form stable, soluble oligomers important for the advancement of knowledge, detection, and treatment of Alzheimer&#39;s disease. Antibodies specific to oligomeric Aβ and their methods of synthesis are also described.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.15/794,776, entitled “Synthetic Beta-Amyloid Peptides Capable of FormingStable Antigenic Oligomers” to Nowick et al., filed Oct. 26, 2017, whichclaims priority to U.S. Provisional Application Ser. No. 62/414,326,entitled “Synthetic Beta-Amyloid Peptides Capable of Stabilized,Cross-Linked Oligomerization” to Nowick et al., filed Oct. 28, 2016,which is incorporated herein by reference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Governmental support under Grant No.GM09762 awarded by the National Institutes of Health. The government hascertain rights in the invention.

REFERENCE TO A SEQUENCE LISTING SUBMITTED ELECTRONICALLY VIA EFS-WEB

The instant application contains a Sequence Listing which has been filedelectronically in ASCII format and is herein incorporated by referencein its entirety. Said ASCII copy, created on Jul. 28, 2020, is named“04843conSeqList_ST25” and is 16,684 bytes in size.

FIELD OF THE INVENTION

The present invention is directed to synthetic peptides and oligomers,and methods of synthesis and applications thereof; and more particularlyto synthetic peptides and stabilized antigenic oligomers that mimicamyloid-beta and higher-order conformations thereof. The presentinvention is also directed to antigen binding molecules thatspecifically and preferentially target soluble amyloid-beta oligomers.

BACKGROUND OF THE INVENTION

Amyloid precursor protein (APP) is an integral membrane proteinexpressed in mammalian neurons. The protein concentrates around synapsesand likely is involved in neural development and synaptogenesis (Rik vander Kant and Lawrence S. B. Goldstein, Dev Cell 2015; 32(4):502-15, thedisclosure of which is incorporated herein by reference). Althoughexpression is highest during development, APP remains expressedthroughout life, possibly regulating lipid reorganization duringsynaptic activity.

APP undergoes extensive and complex proteolytic processing to createseveral peptide fragments. These fragments include μ-amyloid (Aβ),soluble APPα (sAPPα), soluble APPβ (sAPPβ), APP intracellular domain(AICD), c-terminal fragment 99 (C99), c-terminal fragment (C83), and P3.Of particular interest are the Aβ fragments, which are peptidestypically between 30 and 51 amino acids derived from the extracellularportion of APP. The most common Aβ peptides are Aβ₁₋₄₀ and Aβ₁₋₄₂ (FIG.1 and Seq. ID Nos. 1 and 2).

Common features in the neurodegenerative Alzheimer's disease (AD) areoligomerization and fibril aggregation of Aβ in the extracellular spacearound neuronal junctions. Some experts have suggested that solubleoligomeric forms of the peptide are causal in development of the disease(see, I. Benilova, et al. Nat. Neurosci. 2012 15, 349-357; and L. N.Zhao, et al., Int J Mol Sci. 2012 13, 7303-7327; the disclosures ofwhich are incorporated herein by reference). Despite great efforts toresearch and comprehend the relationship between Aβ oligomers and AD,there are still many unanswered and challenging questions regarding thisrelationship.

SUMMARY OF THE INVENTION

Many embodiments are directed a synthetic beta-amyloid peptide thatcomprises a peptide selected from a group consisting of: (1) a peptidehaving a substantially similar sequence to Seq. ID. No. 3; (2) a peptidehaving a substantially similar sequence to Seq. ID. No. 4; (3) a peptideconsisting of a first and a second strand, wherein the first strand hasa sequence substantially similar to Seq. ID No. 5 and the second strandhas a sequence substantially similar to Seq. ID No. 6, wherein the firstand second strand are covalently linked by the delta-amino group of theside chain of the N-terminal ornithine of the first strand to theC-terminus of the second strand, and wherein the first and second strandare also covalently linked by the delta-amino group of the side chain ofthe N-terminal ornithine of the second strand to the C-terminus of thefirst strand; and

(4) a peptide consisting of a first and a second strand, wherein thefirst strand has a sequence substantially similar to Seq. ID No. 7 andthe second strand has a sequence substantially similar to Seq. ID No. 8,wherein the first and second strand are covalently linked by thedelta-amino group of the side chain of the N-terminal ornithine of thefirst strand to the C-terminus of the second strand, and wherein thefirst and second strand are also covalently linked by the delta-aminogroup of the side chain of the N-terminal ornithine of the second strandto the C-terminus of the first strand. It should be understood thatthese embodiments can be restated visually, such that a syntheticbeta-amyloid peptide comprising a peptide having a molecular formulaselected from a group consisting of:

wherein N-terminus is an optional peptide having a sequence selectedfrom a group consisting of Seq. ID No. 9 and Orn₁₆; wherein C-terminusis an optional peptide having a sequence selected from a groupconsisting of Seq. ID No. 10 and Seq. ID No. 11; wherein X₂₂ is an aminoacid selected from a group consisting of E₂₂, Q₂₂, and K₂₂; wherein X₂₃is an amino acid selected from a group consisting of D₂₃ and N₂₃;wherein X₃₅ is an amino acid selected from a group consisting of M₃₅,Orn₃₅, and MetO₃₅; and wherein R is a substituent selected from a groupconsisting of H, Me, alkyl, and aryl.

In more embodiments, a synthetic beta-amyloid peptide further comprisesat least two more synthetic beta-amyloid peptides, wherein threesynthetic beta-amyloid peptides are covalently linked by cysteinedisulfide bridges to form a trimer.

In even more embodiments, the trimer consists of a first, a second, anda third synthetic beta-amyloid peptide; wherein each peptide consists ofa first and a second strand; wherein the first strand has a sequencesubstantially similar to Seq. ID No. 5 and the second strand has asequence substantially similar to Seq. ID No. 6; wherein the first andsecond strand are covalently linked by the delta-amino group of the sidechain of the N-terminal ornithine of the first strand to the C-terminusof the second strand, and wherein the first and second strand are alsocovalently linked by the delta-amino group of the side chain of theN-terminal ornithine of the second strand to the C-terminus of the firststrand; and

(4) a peptide consisting of a first and a second strand, wherein thefirst strand has a sequence substantially similar to Seq. ID No. 7 andthe second strand has a sequence substantially similar to Seq. ID No. 8,wherein the first and second strand are covalently linked by thedelta-amino group of the side chain of the N-terminal ornithine of thefirst strand to the C-terminus of the second strand, and wherein thefirst and second strand are also covalently linked by the delta-aminogroup of the side chain of the N-terminal ornithine of the second strandto the C-terminus of the first strand. It should be understood thatthese embodiments can be restated visually, such that a syntheticbeta-amyloid peptide comprising a peptide having a molecular formulaselected from a group consisting of:

wherein N-terminus is an optional peptide having a sequence selectedfrom a group consisting of Seq. ID No. 9 and Orn₁₆; wherein C-terminusis an optional peptide having a sequence selected from a groupconsisting of Seq. ID No. 10 and Seq. ID No. 11; wherein X₂₂ is an aminoacid selected from a group consisting of E₂₂, Q₂₂, and K₂₂; wherein X₂₃is an amino acid selected from a group consisting of D₂₃ and N₂₃;wherein X₃₅ is an amino acid selected from a group consisting of M₃₅,Orn₃₅, and MetO₃₅; and wherein R is a substituent selected from a groupconsisting of H, Me, alkyl, and aryl.

In more embodiments, a synthetic beta-amyloid peptide further comprisesat least two more synthetic beta-amyloid peptides, wherein threesynthetic beta-amyloid peptides are covalently linked by cysteinedisulfide bridges to form a trimer.

In even more embodiments, the trimer consists of a first, a second, anda third synthetic beta-amyloid peptide; wherein each peptide consists ofa first and a second strand; wherein the first strand has a sequencesubstantially similar to Seq. ID No. 5 and the second strand has asequence substantially similar to Seq. ID No. 6; wherein the first andsecond strand are covalently linked by the delta-amino group of the sidechain of the N-terminal ornithine of the first strand to the C-terminusof the second strand, and wherein the first and second strand are alsocovalently linked by the delta-amino group of the side chain of theN-terminal ornithine of the second strand to the C-terminus of the firststrand. Furthermore, the cysteine in amino acid position two of thefirst strand of the first peptide forms a disulfide linkage with thecysteine in amino acid position six of the first strand of the secondpeptide; and the cysteine in amino acid position two of the first strandof the second peptide forms a disulfide linkage with the cysteine inamino acid position six of the first strand of the third peptide; andthe cysteine in amino acid position two of the first strand of the thirdpeptide forms a disulfide linkage with the cysteine in amino acidposition six of the first strand of the first peptide. It should beunderstood that these embodiments can be restated visually, such thatthe trimer has the molecular formula:

wherein X₂₂ is an amino acid selected from a group consisting of E₂₂,Q₂₂, and K₂₂;

wherein X₂₃ is an amino acid selected from a group consisting of D₂₃ andN₂₃; wherein

X₃₅ is an amino acid selected from a group consisting of M₃₅, Orn₃₅, andMetO₃₅; and

wherein R is a substituent selected from a group consisting of H, Me,alkyl, and aryl.

In further more embodiments, the trimer consists of a first, a second,and a third synthetic beta-amyloid peptide; wherein each consists of afirst and a second strand; wherein the first strand has a sequencesubstantially similar to Seq. ID No. 7 and the second strand has asequence substantially similar to Seq. ID No. 8; wherein the first andsecond strand are covalently linked by the delta-amino group of the sidechain of the N-terminal ornithine of the first strand to the C-terminusof the second strand, and wherein the first and second strand are alsocovalently linked by the delta-amino group of the side chain of theN-terminal ornithine of the second strand to the C-terminus of the firststrand. Furthermore, the cysteine in amino acid position two of thesecond strand of the first peptide forms a disulfide linkage with thecysteine in amino acid position six of the second strand of the secondpeptide; and the cysteine in amino acid position two of the secondstrand of the second peptide forms a disulfide linkage with the cysteinein amino acid position six of the second strand of the third peptide;and the cysteine in amino acid position two of the second strand of thethird peptide forms a disulfide linkage with the cysteine in amino acidposition six of the second strand of the first peptide.

In even further more embodiments, at least one synthetic beta-amyloidpeptide incorporates an ornithine in the amino acid position thatcorresponds to methionine35 of a naturally occurring beta-amyloidpeptide.

In even further more embodiments, at least one central amino acid isN-methylated.

In even further more embodiments, the synthetic beta-amyloid peptide hasat least one amino acid mutation that corresponds to familialAlzheimer's disease.

Many embodiments are directed to a method of producing antibodies havingaffinity for soluble beta-amyloid oligomers that comprises administeringan immunocompetent animal with an immunogenic cocktail comprisingsynthetic crosslinked beta-amyloid trimers, wherein at least one trimerconsists of three beta-amyloid peptides; wherein each peptide of the atleast one trimer has the same sequence: and wherein each peptide of theat least one trimer is selected from the group consisting of: (1) apeptide having a substantially similar sequence to Seq. ID. No. 3; (2) apeptide having a substantially similar sequence to Seq. ID. No. 4; (3) apeptide consisting of a first and a second strand, wherein the firststrand has a sequence substantially similar to Seq. ID No. 5 and thesecond strand has a sequence substantially similar to Seq. ID No. 6,wherein the first and second strand are covalently linked by thedelta-amino group of the side chain of the N-terminal ornithine of thefirst strand to the C-terminus of the second strand, and wherein thefirst and second strand are also covalently linked by the delta-aminogroup of the side chain of the N-terminal ornithine of the second strandto the C-terminus of the first strand; and (4) a peptide consisting of afirst and a second strand, wherein the first strand has a sequencesubstantially similar to Seq. ID No. 7 and the second strand has asequence substantially similar to Seq. ID No. 8, wherein the first andsecond strand are covalently linked by the delta-amino group of the sidechain of the N-terminal ornithine of the first strand to the C-terminusof the second strand, and wherein the first and second strand are alsocovalently linked by the delta-amino group of the side chain of theN-terminal ornithine of the second strand to the C-terminus of the firststrand. It should be understood that these embodiments can be restatedvisually, such that a method of producing antibodies having affinity forsoluble beta-amyloid oligomers comprises administering animmunocompetent animal with an immunogenic cocktail comprising syntheticcrosslinked beta-amyloid trimers, wherein at least one trimer consistsof three beta-amyloid peptides having a molecular formula selected froma group consisting of:

wherein N-terminus is an optional peptide having a sequence selectedfrom a group consisting of Seq. ID No. 9 and Orn₁₆; wherein C-terminusis an optional peptide having a sequence selected from a groupconsisting of Seq. ID No. 10 and Seq. ID No. 11; wherein X₂₂ is an aminoacid selected from a group consisting of E₂₂, Q₂₂, and K₂₂; wherein X₂₃is an amino acid selected from a group consisting of D₂₃ and N₂₃;wherein X₃₅ is an amino acid selected from a group consisting of M₃₅,Orn₃₅, and MetO₃₅; and wherein R is a substituent selected from a groupconsisting of H, Me, alkyl, and aryl.

In more embodiments, a method of producing antibodies further comprisesharvesting antibodies from the immunocompetent animal.

In even more embodiments, a method of producing antibodies furthercomprises repeating administration of beta-amyloid trimers to theimmunocompetent animal.

In further more embodiments, the immunocompetent animal is selected fromthe group consisting of human, rabbit, goat, mouse, rat, chicken, andguinea pig.

In even further more embodiments, the immunogenic cocktail furthercomprises an adjuvant.

In even further more embodiments, the adjuvant is Freund's adjuvant.

In even further more embodiments, the at least one beta-amyloid trimeris conjugated with hemocyanin.

In even further more embodiments, the immunocompetent animal is a humanindividual for the purpose of vaccination.

Many embodiments are direct to a method to purify antibodies thatcomprises having antigen binding molecules in solution. Passing theantigen binding molecules through an affinity chromatography solidphase; wherein the solid phase comprises synthetic crosslinkedbeta-amyloid trimers able to capture the antigen binding molecules,wherein at least one beta-amyloid trimer consists of three beta-amyloidpeptides; wherein each beta-amyloid peptide of the at least one trimerhas the same peptide sequence; wherein each peptide of the at least onetrimer is selected from the group consisting of (1) a peptide having asubstantially similar sequence to Seq. ID. No. 3; (2) a peptide having asubstantially similar sequence to Seq. ID. No. 4; (3) a peptideconsisting of a first and a second strand, wherein the first strand hasa sequence substantially similar to Seq. ID No. 5 and the second strandhas a sequence substantially similar to Seq. ID No. 6, wherein the firstand second strand are covalently linked by the delta-amino group of theside chain of the N-terminal ornithine of the first strand to theC-terminus of the second strand, and wherein the first and second strandare also covalently linked by the delta-amino group of the side chain ofthe N-terminal ornithine of the second strand to the C-terminus of thefirst strand; and (4) a peptide consisting of a first and a secondstrand, wherein the first strand has a sequence substantially similar toSeq. ID No. 7 and the second strand has a sequence substantially similarto Seq. ID No. 8, wherein the first and second strand are covalentlylinked by the delta-amino group of the side chain of the N-terminalornithine of the first strand to the C-terminus of the second strand,and wherein the first and second strand are also covalently linked bythe delta-amino group of the side chain of the N-terminal ornithine ofthe second strand to the C-terminus of the first strand. Eluting thecaptured antibodies from the solid phase using a buffer capable ofdissociating the captured antibodies from the synthetic crosslinkedbeta-amyloid trimers. It should be understood that these embodiments canbe restated visually, such that a method to purify antibodies compriseshaving antigen binding molecules in solution. Passing the antigenbinding molecules through an affinity chromatography solid phase,wherein the solid phase comprises synthetic crosslinked beta-amyloidtrimers able to capture the antigen binding molecules, wherein thebeta-amyloid trimers comprise at least three beta-amyloid peptideshaving a molecular formula selected from a group consisting of:

wherein N-terminus is an optional peptide having a sequence selectedfrom a group consisting of Seq. ID No. 9 and Orn₁₆; wherein C-terminusis an optional peptide having a sequence selected from a groupconsisting of Seq. ID No. 10 and Seq. ID No. 11; wherein X₂₂ is an aminoacid selected from a group consisting of E₂₂, Q₂₂, and K₂₂; wherein X₂₃is an amino acid selected from a group consisting of D₂₃ and N₂₃;wherein X₃₅ is an amino acid selected from a group consisting of M₃₅,Orn₃₅, and MetO₃₅; and wherein R is a substituent selected from a groupconsisting of H, Me, alkyl, and aryl.

In more embodiments, the antigen binding molecules are a type ofmolecules selected from the group consisting of polyclonal antibodies,monoclonal antibodies, multispecific antibodies, human antibodies,humanized antibodies, primatized antibodies, chimeric antibodies, singlechain antibodies, and epitope-binding fragments of antibodies.

In even more embodiments, the antigen binding molecules are antibodiesgenerated in an immunocompetent animal.

In further more embodiments, the antibodies are generated byadministering the immunocompetent animal with an immunogenic cocktailcomprising synthetic crosslinked beta-amyloid trimers; wherein at leastone beta-amyloid trimer consists of three beta-amyloid peptides; whereineach peptide of the at least one trimer has the same sequence: andwherein each peptide of the at least one trimer is selected from thegroup consisting of (1) a peptide having a substantially similarsequence to Seq. ID. No. 3; (2) a peptide having a substantially similarsequence to Seq. ID. No. 4; (3) a peptide consisting of a first and asecond strand, wherein the first strand has a sequence substantiallysimilar to Seq. ID No. 5 and the second strand has a sequencesubstantially similar to Seq. ID No. 6, wherein the first and secondstrand are covalently linked by the delta-amino group of the side chainof the N-terminal ornithine of the first strand to the C-terminus of thesecond strand, and wherein the first and second strand are alsocovalently linked by the delta-amino group of the side chain of theN-terminal ornithine of the second strand to the C-terminus of the firststrand; and (4) a peptide consisting of a first and a second strand,wherein the first strand has a sequence substantially similar to Seq. IDNo. 7 and the second strand has a sequence substantially similar to Seq.ID No. 8, wherein the first and second strand are covalently linked bythe delta-amino group of the side chain of the N-terminal ornithine ofthe first strand to the C-terminus of the second strand, and wherein thefirst and second strand are also covalently linked by the delta-aminogroup of the side chain of the N-terminal ornithine of the second strandto the C-terminus of the first strand. It should be understood thatthese embodiments can be restated visually, such that the antibodies aregenerated by administering the immunocompetent animal with animmunogenic cocktail comprising synthetic crosslinked beta-amyloidtrimers; wherein at least one trimer consists of three beta-amyloidpeptides having a molecular formula selected from a group consisting of:

wherein N-terminus is an optional peptide having a sequence selectedfrom a group consisting of Seq. ID No. 9 and Orn₁₆; wherein C-terminusis an optional peptide having a sequence selected from a groupconsisting of Seq. ID No. 10 and Seq. ID No. 11; wherein X₂₂ is an aminoacid selected from a group consisting of E₂₂, Q₂₂, and K₂₂; wherein X₂₃is an amino acid selected from a group consisting of D₂₃ and N₂₃;wherein X₃₅ is an amino acid selected from a group consisting of M₃₅,Orn₃₅, and MetO₃₅; and wherein R is a substituent selected from a groupconsisting of H, Me, alkyl, and aryl.

In even further more embodiments, the eluted antigen binding moleculeshave higher affinity for a soluble oligomer of naturally occurringbeta-amyloid than both a monomer of naturally occurring beta-amyloid andan insoluble fibril of naturally occurring beta-amyloid.

In even further more embodiments, the oligomer of naturally occurringbeta-amyloid is an oligomer selected from a group consisting of trimers,hexamers, and dodecamers.

In even further more embodiments, the antibodies are derived from anantibody producing cell sourced from a human subject.

In even further more embodiments, the human subject is of at least 65years of age, having full cognitive capacity, good health, and noclinical signs of dementia.

In even further more embodiments, wherein the antibody producing cell isselected from a group consisting of B cells, B memory cells, hybridomas,and recombinant host cells expressing at least one antibody.

Additional embodiments and features are set forth in part in thedescription that follows, and in part will become apparent to thoseskilled in the art upon examination of the specification or may belearned by the practice of the disclosed subject matter. A furtherunderstanding of the nature and advantages of the present disclosure maybe realized by reference to the remaining portions of the specificationand the drawings, which forms a part of this disclosure.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee. These and other features and advantages of thepresent invention will be better understood by reference to thefollowing detailed description when considered in conjunction with theaccompanying drawings where:

FIG. 1 provides a schematic detailing the amino acid sequence ofbeta-amyloid (Aβ).

FIG. 2 provides a schematic explaining the higher-order structure of Aβpeptides.

FIGS. 3A and 3B provide molecular structure diagrams detailing thechemical structure and peptide sequence of synthetic Aβ peptides withcysteine substitutions in accordance with various embodiments of theinvention.

FIGS. 4A and 4B provide molecular structure diagrams detailing thechemical structure and peptide sequence of synthetic crosslinked Aβpeptides with cysteine substitutions in accordance with variousembodiments of the invention.

FIGS. 5 and 6 provide molecular structure diagrams detailing thechemical structure and peptide sequence of synthetic crosslinked Aβtrimers with cysteine substitutions in accordance with variousembodiments of the invention.

FIGS. 7A and 7B provide schematics detailing the important amino acidsfor β-hairpin formation in Aβ peptides.

FIG. 8 provides a schematic detailing the structure of a syntheticcrosslinked Aβ trimer in accordance with various embodiments of theinvention.

FIG. 9 provides a schematic detailing the structure of a hexamer formedfrom two synthetic crosslinked Aβ trimers in accordance with variousembodiments of the invention.

FIG. 10 provides a schematic detailing the structure of a dodecamerformed from four synthetic crosslinked Aβ trimers in accordance withvarious embodiments of the invention.

FIG. 11 provides a schematic detailing the structure of an annular porelike structure formed from twenty-four synthetic crosslinked Aβ trimersin accordance with various embodiments of the invention.

FIG. 12 provides molecular structure diagrams detailing the chemicalstructure and peptide sequence of synthetic Aβ peptides in accordancewith various embodiments of the invention.

FIG. 13 provides molecular structure diagrams detailing the chemicalstructure and peptide sequence of synthetic Aβ peptides with offsetβ-hairpin hydrogen binding in accordance with various embodiments of theinvention.

FIG. 14 provides a process to generate antibodies using Aβ trimers inaccordance with various embodiments of the invention.

FIG. 15A provides a molecular structure diagram detailing the chemicalstructure and peptide sequence of peptide 1 in accordance with variousembodiments of the invention.

FIG. 15B provides a molecular structure diagram detailing the chemicalstructure and peptide sequence of peptide 2 in accordance with variousembodiments of the invention.

FIG. 16A provides an X-ray crystallographic schematic detailing thestructure of a synthetic crosslinked Aβ trimer generated using peptide 1in accordance with various embodiments of the invention.

FIG. 16B provides an X-ray crystallographic schematic detailing thestructure of a synthetic crosslinked Aβ trimer generated using peptide 2in accordance with various embodiments of the invention.

FIG. 17A provides a molecular structure diagram detailing the chemicalstructure and peptide sequence of peptide 3 in accordance with variousembodiments of the invention.

FIG. 17B provides a molecular structure diagram detailing the chemicalstructure and peptide sequence of peptide 4 in accordance with variousembodiments of the invention.

FIG. 18 provides schematics of various structures that canhypothetically be generated by crosslinking Aβ peptides havingcysteines.

FIG. 19A provides a molecular structure diagram detailing the chemicalstructure and peptide sequence of trimer 3 generated from peptide 3 inaccordance with various embodiments of the invention.

FIG. 19B provides a molecular structure diagram detailing the chemicalstructure and peptide sequence of trimer 4 generated from peptide 4 inaccordance with various embodiments of the invention.

FIG. 20A provides a graphical representation of reverse-phase HPLCelutes produced by crosslinking peptide 3 in accordance with variousembodiments of the invention.

FIG. 20B provides a graphical representation of reverse-phase HPLCelutes produced by crosslinking peptide 4 in accordance with variousembodiments of the invention.

FIG. 21 provides an X-ray crystallographic schematic detailing thechemical structure of trimer 3 in accordance with various embodiments ofthe invention.

FIG. 22 provides an X-ray crystallographic schematic detailing thechemical structure of trimer 3, zoomed in on the trimer-trimer contactpoint, in accordance with various embodiments of the invention.

FIGS. 23A, 23B and 23C provide X-ray crystallographic schematicsdetailing the chemical structure of hexamers and columns formed bytrimer 3, generated in accordance with various embodiments of theinvention.

FIG. 24 provides an X-ray crystallographic schematic detailing thechemical structure of trimer 4 in accordance with various embodiments ofthe invention.

FIG. 25 provides an X-ray crystallographic schematic detailing thechemical structure of trimer 4, zoomed in on the trimer-trimer contactpoint, in accordance with various embodiments of the invention.

FIG. 26 provides an X-ray crystallographic schematic detailing adodecamer formed by trimer 4, generated in accordance with variousembodiments of the invention.

FIGS. 27A, 27B and 27C provide X-ray crystallographic schematicsdetailing an annular pore formed by trimer 4, generated in accordancewith various embodiments of the invention.

FIG. 28A provides an image of a silver stain demonstrating that Aβ₁₋₄₂forms oligomers.

FIG. 28B provides a data graph demonstrating that Aβ₁₋₄₂ is toxic toSH-SY5Y cells.

FIG. 29A provides a data graph detailing the toxicity of peptides 1 and2 and trimers 3 and 4 to SH-SY5Y cells, generated in accordance withvarious embodiments of the invention.

FIG. 29B provides a data graph demonstrating that peptide 4 is not toxicto SH-SY5Y cells.

FIG. 30A provides a data graph detailing the toxicity of peptides 1 and2 and trimers 3 and 4 to SH-SY5Y cells, generated in accordance withvarious embodiments of the invention.

FIG. 30B provides a dot blot detailing trimers 3 and 4, but not peptides1 and 2, are recognizable by the A11 antibody, generated in accordancewith embodiments of the invention.

FIG. 31A provides a data graph of size exclusion chromatography ofpeptides 1 and 2, trimers 3 and 4, and other reference proteins,generated in accordance with embodiments of the invention.

FIG. 31B provides a silver stain of an SDS-PAGE gel of peptides 1 and 2and trimers 3 and 4 that were ran through an electrophoresis apparatus,generated in accordance with various embodiments of the invention.

FIG. 31C provides a data graph of circular dichroism spectra of peptides1 and 2 and trimers 3 and 4, generated in accordance with variousembodiments of the invention.

FIG. 32A provides schematics of three different β-hairpins formed byAβ₁₅₋₃₆, with different residue pairings.

FIG. 32B provides molecular structure diagrams detailing the chemicalstructure and peptide sequence of peptides 5-7 in accordance withvarious embodiments of the invention.

FIG. 33A provides an X-ray crystallographic schematic detailing thechemical structure of a trimer formed by peptide 5, generated inaccordance with various embodiments of the invention.

FIG. 33B provides an X-ray crystallographic schematic detailing thechemical structure of a dodecamer formed by peptide 5, generated inaccordance with various embodiments of the invention.

FIG. 33C provides an X-ray crystallographic schematic detailing thechemical structure of a sandwich-like hexamer formed by peptide 5,generated in accordance with various embodiments of the invention.

FIG. 33D provides an X-ray crystallographic schematic detailing thechemical structure of a ball-shaped dodecamer formed by peptide 6,generated in accordance with various embodiments of the invention.

FIGS. 33E and 33F provide X-ray crystallographic schematics detailingthe chemical structure of two types of trimers within the dodecamerformed by peptide 6, generated in accordance with various embodiments ofthe invention.

FIG. 34 provides X-ray crystallographic schematics detailing thechemical structure of dodecamers formed by peptides 5 and 6, generatedin accordance with various embodiments of the invention.

FIGS. 35 and 36 provide X-ray crystallographic schematics detailing thechemical structure of fibril-like assemblies formed by peptide 7,generated in accordance with various embodiments of the invention.

FIG. 37 provides a generic molecular structure diagram detailing thechemical structure and peptide sequence of a β-hairpin peptide.

FIG. 38 provides molecular structure diagrams detailing the chemicalstructure and peptide sequence of Aβ₁₇₋₃₆ hairpin and peptide 2 inaccordance with various embodiments of the invention.

FIG. 39 provides an X-ray crystallographic schematic detailing thechemical structure of a trimer formed by peptide 2, generated inaccordance with various embodiments of the invention.

FIG. 40 provides molecular structure diagrams detailing the chemicalstructure and peptide sequence of Aβ₁₆₋₃₆ hairpin and peptide 8 inaccordance with various embodiments of the invention.

FIG. 41A provides a silver stain of an SDS-PAGE gel of peptides 2 and8-10 and trimers 3 and 4 that were ran through an electrophoresisapparatus, generated in accordance with various embodiments of theinvention.

FIG. 41B provides a data graph of size exclusion chromatography ofpeptides 2 and 8 and other reference proteins, generated in accordancewith embodiments of the invention.

FIG. 42 provides X-ray crystallographic schematics detailing thechemical structures of the major and minor surfaces of peptides 2 and 8in accordance with various embodiments of the invention.

FIG. 43 provides X-ray crystallographic schematics detailing thechemical structures of hexamers formed by peptide 8, generated inaccordance with various embodiments of the invention.

FIG. 44 provides X-ray crystallographic schematics detailing thechemical structures of hexamers formed by peptide 8, generated inaccordance with various embodiments of the invention.

FIG. 45 provides X-ray crystallographic schematics detailing thechemical structures of hexamers formed by peptides 2 and 8, generated inaccordance with various embodiments of the invention.

FIG. 46A provides an X-ray crystallographic schematic detailing thechemical structures of dimers formed by peptide 8, generated inaccordance with various embodiments of the invention.

FIG. 46B provides a molecular structure diagram detailing the chemicalstructure and peptide sequence of a dimer formed by peptide 8, generatedin accordance with various embodiments of the invention.

FIG. 47 provides X-ray crystallographic schematics detailing thechemical structures of the major and minor surfaces of a dimer formed bypeptide 8, generated in accordance with various embodiments of theinvention.

FIG. 48A provides an X-ray crystallographic schematic detailing thechemical structure of a trimer formed by peptide 8, generated inaccordance with various embodiments of the invention.

FIG. 48B provides an X-ray crystallographic schematic detailing thechemical structure of a corner of a trimer formed by peptide 8,generated in accordance with various embodiments of the invention.

FIG. 49 provides X-ray crystallographic schematics detailing thechemical structures of the major and minor surfaces of a trimer formedby peptide 8, generated in accordance with various embodiments of theinvention.

FIG. 50A provides a molecular structure diagram detailing the chemicalstructure and peptide sequence of peptide 9 in accordance with variousembodiments of the invention.

FIG. 50B provides a molecular structure diagram detailing the chemicalstructure and peptide sequence of peptide 10 in accordance with variousembodiments of the invention.

FIG. 51 provides X-ray crystallographic schematics detailing thechemical structures of the minor surfaces of peptides 2, 8, and 10 inaccordance with various embodiments of the invention.

FIG. 52A provides an X-ray crystallographic schematic detailing thechemical structure of the antiparallel β-sheet formed by peptide 10 inaccordance with various embodiments of the invention.

FIG. 52B provides an X-ray crystallographic schematic detailing thechemical structure of a column of laminated antiparallel β-sheet dimersformed by peptide 10, generated in accordance with various embodimentsof the invention.

FIG. 53 provides a data graph detailing the toxicity of peptides 2 and9-10 to SH-SY5Y cells, generated in accordance with various embodimentsof the invention.

FIG. 54 provides a crystallographically based model of an Aβ₁₂₋₄₀barrel-like hexamer, generated in accordance with various embodiments ofthe invention.

FIG. 55 provides a dot blot detailing affinity purified antibodies havehigh affinity for trimers 3 and 4, but not peptides 1 and 2, generatedin accordance with embodiments of the invention.

FIG. 56 provides a data graph of an ELISA experiment detailing affinitypurified antibodies have high affinity for trimers 3 and 4, but notpeptides 1 and 2, generated in accordance with embodiments of theinvention.

FIG. 57 provides an image of a Western blot detailing affinity purifiedantibodies recognizing oligomers of Aβ₁₋₄₀ and Aβ₁₋₄₂ of brain extractsfrom Alzheimer's disease and healthy individuals, generated inaccordance with embodiments of the invention.

FIG. 58 provides an image of a Western blot detailing affinity purifiedantibodies, but not the 6E10 antibody, preferentially recognizeoligomers of Aβ₁₋₄₀ and Aβ₁₋₄₂, generated in accordance with embodimentsof the invention.

FIG. 59 provides fluorescent microscopic images of Alzheimer's diseaseand healthy brain tissue slices using affinity purified antibodies,generated in accordance with embodiments of the invention.

FIG. 60 provides fluorescent microscopic images of Tg2576 and wild-typemice brain tissue slices using affinity purified antibodies, generatedin accordance with embodiments of the invention.

FIG. 61 provides X-ray crystallographic schematic detailing the abilityof crystal violet dye molecules to integrate into a crosslinked trimer4, generated in accordance with various embodiments of the invention.

FIG. 62A provides an image showing the difference in absorbance ofcrystal violet dye with and without crosslinked trimer 4, generated inaccordance with various embodiments of the invention.

FIG. 62B provides a data graph detailing the absorbance spectra ofcrystal violet dye with various concentrations of crosslinked trimer 4,generated in accordance with various embodiments of the invention.

FIG. 63A provides an image showing the fluorescence of crystal violetdye with crosslinked trimer 4, generated in accordance with variousembodiments of the invention.

FIG. 63B provides a data graph detailing the fluorescence spectra ofcrystal violet dye with various concentrations of crosslinked trimer 4,generated in accordance with various embodiments of the invention.

DETAILED DISCLOSURE OF THE INVENTION

Turning now to the diagrams and figures, synthetic beta-amyloid (Aβ)peptides capable of forming stable oligomers, and synthesis thereof, aredescribed. Embodiments of the invention are directed to synthetic Aβpeptides that are modified from the naturally occurring Aβ found innature. Some of these embodiments include peptides having a substitutedcysteine amino acid in place of a naturally occurring amino acid.Particular Aβ peptide embodiments incorporate the cysteine into aminoacid position 17 or 21.

Many other embodiments of the invention are directed to other Aβ peptidemodifications; these may include truncation and removal of amino acids,N-methylation of amino acids, covalent linkage of peptides by δ-linkedornithine (^(δ)Orn) turn mimics, substitution of hydrophobic amino acidswith a hydrophilic isostere, or incorporation of amino acidsubstitutions that correspond with familial version of Alzheimer'sdisease (AD). In some particular embodiments, the N-terminal region orC-terminal region of the Aβ peptide can be removed. For example,embodiments of the invention include a truncated Aβ₁₇₋₃₆ peptide andthus amino acids 1-16 and 37-42 have been removed. In other particularembodiments, amino acids 24-29 are removed to yield distinct N-terminaland C-terminal Aβ peptides. In other embodiments, other truncated Aβpeptides are possible, such as those to mimic Aβ₁₆₋₃₆ and Aβ₁₅₋₃₆. Thevarious truncations may be combined or in solitude. In addition, anumber of embodiments will have a ^(δ)Orn turn mimic to replace thetruncated portion of the Aβ peptide. For example, embodiments may have aturn mimic link the N-terminus of Alanine at position 30 (A₃₀) with theC-terminus of another amino acid of the peptide (e.g., Aspartate atposition 23 (D₂₃)). A similar embodiment may have a ^(δ)Orn linkagebetween the N-terminus of Leucine at position 17 (L₁₇) and theC-terminus of another amino acid (e.g., Valine at position 36 (V₃₆)).Other embodiments are directed to methylation of the amide of certainamino acids of the Aβ peptide. The methylation can help prevent improperaggregation and fibril formation of the peptides. In particularembodiments, central and outer amides of the Aβ β-hairpin aremethylated. In some embodiments, Phenylalanine at position 20 (F₂₀),Phenylalanine at position 19 (F₁₉) or Glycine at position 33 (G₃₃) of Aβare N-methylated. Other embodiments are directed to increasing thesolubility of the peptide by exchanging a hydrophobic amino acid with ahydrophilic isostere. For example, embodiments are direct to Aβ peptidesthat have substituted the hydrophilic Ornithine at position 35 (Orn₃₅)in place of the naturally occurring hydrophobic Methionine (M₃₅) thatcorresponds to naturally occurring Aβ peptides. More embodiments aredirected to synthetic Aβ peptides that incorporate amino acidsubstitutions corresponding with familial AD. In particular, embodimentsare directed to Aβ peptides that incorporate known AD mutations,including the Dutch (E22Q), the Iowa (D23N), the Dutch Iowa (E22Q,D23N), the Italian (E22K), and the Osaka (E22del) mutations.

Various embodiments of the invention are also directed to the ability ofsynthetic Aβ peptides to form secondary structures and tertiaryconformations. In several embodiments, the synthetic Aβ peptides form acomplementary β-hairpin secondary structure. In accordance with otherembodiments, tertiary structures are produced by the Aβ peptides thatare higher-order oligomers composed of Aβ monomers. Disulfidecrosslinking between modified Aβ peptides with cysteine substitutionsassist in the formation, stability, or homogeneity of oligomers of manyembodiments. Likewise, embodiments are directed to oligomers that aretrimers, hexamers, dodecamers, or annular-pore complexes.

Many other embodiments of the invention are directed to properties orapplications of use of synthetic Aβ peptides and oligomers. Manyembodiments are directed to Aβ peptides having advantageous properties,including, but not limited to, solubility, cytotoxicity, neurotoxicity,synaptotoxicity, antigenicity, or ability to be targeted by smallmolecules. As such, embodiments are directed to Aβ peptides andoligomers that remain soluble and do not aggregate to form fibrils.Other embodiments are directed to Aβ peptides and oligomers that aretoxic to neuronal cells and disrupt synapse connections. Even otherembodiments are directed to the ability to design and produce polyclonalor monoclonal antibodies that bind to synthetic or natural Aβ peptidesand oligomers. And even other embodiments are directed to the ability todesign small molecule probes or drugs that have an effect on Aβ peptidesand oligomers.

More embodiments are direct to antigen binding molecules that have highspecificity, preference, and affinity towards soluble oligomers of Aβ.In many of these embodiments, the antigen binding molecules have lowaffinity for Aβ monomers and insoluble fibrils. Various embodimentsinclude monoclonal or polyclonal antibodies that may be derived from anumber of methodologies. In some embodiments, stable crosslinked trimersmay be injected into an animal to stimulate an immune response toproduce antibodies. In additional embodiments, antigen binding moleculesmay be selected and/or purified based on their affinity to crosslinkedtrimers.

Synthetic Aβ Peptides Capable of Crosslinking

In its naturally derived form, Aβ can form peptides of 40 (Aβ₄₀) and 42(Aβ₄₂) amino acids (FIG. 1 and Seq. ID Nos. 1 and 2). These naturallyoccurring peptide monomers are known to form tertiary conformations,including soluble oligomers and insoluble fibrils (FIG. 2). While theinsoluble Aβ fibrils form biologically inactive plaques, the Aβoligomers have been shown to cause neurotoxicity and synaptotoxicitythat may be responsible for neurodegeneration in AD. Although it isdifficult to control the tertiary conformation of Aβ peptides, it wouldbe beneficial to prevent the formation of fibrils and promote theformation of oligomers for further application. As such, embodiments ofthe invention are directed to synthetic Aβ peptides modified from thenaturally occurring Aβ peptide capable of solubility and oligomerformation. Furthermore, embodiments of the peptide also have thecapability of preventing fibril formation and uncontrolled aggregation.

Some embodiments are directed to a synthetic Aβ peptide with cysteinesubstitutions, replacing some of the naturally occurring amino acids. Inmany of these embodiments, a cysteine in one synthetic Aβ peptide iscapable of forming disulfide bond with a cysteine of another syntheticAβ peptide. The disulfide bond formation, in many embodiments, can helpformulate and stabilize a crosslinked trimer conformation, such thatthree synthetic Aβ peptides conform into a triangular shape, eachmonomer linked to another by a disulfide bridge.

FIGS. 3A to 4B depict some particular embodiments of synthetic Aβpeptides with cysteine substitutions (Seq. ID Nos. 3-8). As shown inFIGS. 3A and 4A, cysteines have been incorporated into amino acidpositions 17 and 21, replacing the naturally occurring amino acids L₁₇and A₂₁ (Seq. ID Nos. 3 and 5). These cysteines assist formulation andstabilization of a trimer conformation between three monomeric syntheticAβ peptides (FIGS. 5 and 6). Specifically, the formation of a trimeroccurs when a disulfide bond is formed between C₁₇ of a first monomerand the C₂₁ of a second monomer. The same bond is repeated between thesecond monomer and a third, and again with the third monomer and thefirst. This trimer formation helps to form a stable triangular-likeshape that is resistant to fibril formation and uncontrolledaggregation.

Although FIGS. 3A and 4A depict cysteine substitutions in amino acidposition 17 and 21, other substitutions are possible. For example,replacing A₃₀ and L₃₄ with cysteines will also result in a peptidecapable of forming a triangular trimer that is stable and resistant tofibril formation (FIGS. 3B and 4B; Seq. ID Nos. 4 and 8). It is possiblethat other amino acids could be substituted with cysteines as well,however proper location of the cysteines is necessary to ensure properdistance between the bridged cysteines for quality bond formation andstable conformation.

Several more embodiments are directed to further modification ofsynthetic Aβ peptides. Modifications include truncation and removal ofamino acids, N-methylation of amino acids, covalent linkage of peptidesby ^(δ)Orn turn mimics, and substitution of hydrophobic amino acids witha hydrophilic isostere. The modifications may assist with solubility,stable oligomer formation, prevention of uncontrolled aggregation, orease of synthesis.

Many embodiments are directed to synthetic Aβ peptides that aretruncated with portions of naturally occurring amino acids removed.Truncation of the peptides has several benefits, including, but notlimited to, facilitating synthesis of the peptide, removing unnecessaryamino acids for oligomer formation, and increasing solubility.Truncation of the peptide can vary and still obtain equivalent orsimilar results. Some important peptides for Aβ β-hairpin formation areamino acids 17-23 and 30-36, respectively (See FIGS. 7A and 7B). Thus,the Aβ peptide can be truncated at the N-terminal end from amino acidposition 1 to approximately amino acid position 16 (Seq. ID No. 9), atthe C-terminal end from approximately amino acid position 37 to aminoacid position 40/42 (Seq. ID Nos. 10 and 11), and within the peptidebetween approximately amino acid 24 to approximately amino acid 29 (SeeFIGS. 3A-4B and 7B; Seq. ID Nos. 3-8). In accordance with theseprinciples, embodiments are directed to Aβ peptide truncations thatremove amino acids that are unnecessary for β-hairpin formation,including any N-terminal amino acids, C-terminal amino acids, orinternal amino acids.

More embodiments of synthetic Aβ peptides are directed to stabilizationof β-hairpin formation. As described in the preceding paragraph,important amino acids for β-hairpin formation include 17-23 or 30-36 andunnecessary amino acids can be removed. In various formulations of theseembodiments, the β-hairpins can be covalently linked by an N-terminal^(δ)Orn on one β-strand peptide to the opposing, anti-parallel β-strandpeptide such that the β-amino group of the ornithine side chain iscovalently bonded to the C-terminus of the opposing, anti-parallelβ-strand peptide (see FIGS. 4A and 4B; Seq. ID Nos. 5-8). The ^(δ)Ornturn mimic stabilizes the interactions (e.g., hydrogen bonds) betweenthe β-strand peptides, ensuring a stable conformation. ^(δ)Orn alsoprovides an alternative to replace the naturally occurring Aβ aminoacids when the peptide is truncated. Specifically, various embodimentshave a ^(δ)Orn inserted into amino acid position 16 to covalently linkamino acid 16 with the C-terminus of amino acid 36, effectivelyeliminating the native C and N-termini (FIGS. 3A-4B; Seq. ID Nos. 3-5and 7). In addition, other embodiments have a ^(δ)Orn inserted intoamino acid position 29 to covalently link amino acid 29 with theC-terminus of amino acid 23, effectively eliminating the amino acids 24to 29 (FIGS. 4A and 4B; Seq. ID Nos. 6 and 8). Accordingly, manyembodiments are directed to ^(δ)Orn turn mimics that covalently linkopposing, anti-parallel β-strand peptides, and more specifically to anN-terminal ^(δ)Orn covalent linkage of a peptide strand to theC-terminus of the anti-parallel peptide strand.

Further embodiments of synthetic Aβ peptides inhibit fibril formationand uncontrolled aggregation by modifying the peptides with functionalgroups that promote steric hindrance. Fibril formation and uncontrolledaggregation of Aβ peptides occur when the β-strands of peptides align ina parallel, stacked formation, much like a ladder (R. N. Rambaran and L.C. Serpell, Prion 2008, 2, 112-117, the disclosure of which isincorporated herein by reference). This stacking promotes aggregation ofAβ peptides in an uncontrolled and infinitive manner. One way to preventthis aggregation is to substitute alkyl (e.g., methyl), aryl (e.g.,benzyl, nitrobenzyl) or other similarly bulky groups with an H on one ofthe amides of a central amino acid having an outward-facing amide thatis not involved in β-hairpin hydrogen bonding (see FIGS. 3A-4B; Seq. IDNos. 3-8). The bulky group can be substituted on either β-strand, butshould not interfere with trimer formation. As shown in FIGS. 3A to 4B,amino acids F₂₀ and G₃₃ are good candidates for N-methylation inaccordance with a number of embodiments. The addition of bulky groups tothe peptide backbone sterically hinders the interaction and stacking ofβ-strands and thus prevents uncontrolled aggregation of Aβ peptides intofibrils. As such, various embodiments are directed to synthetic Aβpeptides with bulky functional groups attached to the peptide backbonethat promote steric hindrance, and more specifically to synthetic Aβpeptides with N-methylated amino acids.

Various embodiments also incorporate methods to improve solubility,which is a factor to improve oligomerization and prevent fibrilaggregation. To increase solubility, hydrophobic amino acids can besubstituted with hydrophilic amino acids. Ideally, in order to keepsimilar secondary and tertiary structure, isosteric hydrophilic aminoacid replacements are preferred, but any suitable hydrophilic amino acidwill suffice. Another method to increase solubility is to incorporateoxidized variations of amino acids. For example, a methionine can beoxidized to or substituted with ornithine, methionine sulfoxide ormethionine sulfone (e.g., Met₃₅→Orn₃₅, Met₃₅→MetO₃₅). Accordingly,embodiments are directed to replacement of hydrophobic amino acids withhydrophilic amino acids, and more specifically to isosteric hydrophilicamino acid replacements. More embodiments are directed to oxidation ofvarious amino acids or replacement of amino acids with an oxidizedequivalent (see FIGS. 3A-4B; Seq. ID Nos. 3, 4, 6, and 8). And morespecifically, a number of embodiments are directed to incorporating anornithine in the amino acid position that corresponds to M₃₅ ofnaturally occurring beta-amyloid peptides.

Many other embodiments are directed to modifications that mimic aspectsof AD. Mutations can occur in the Aβ region of the APP gene that resultin altered amino acid composition (I. Benilova, et al., Nat. Neurosci.2012, 15, 349-357, the disclosure of which is incorporated herein byreference). Many of these mutations are highly correlated with familialforms of AD. Thus, Aβ peptides and oligomers that incorporate thesemutations are beneficial to study and develop tools that targetAD-related peptides. Accordingly, embodiments are directed to syntheticAβ peptides that reflect familial AD peptides. In particular, syntheticAβ peptide embodiments incorporate familial mutations that occur withinthe β-hairpin region of the peptide. Many mutations are known to occurwithin this region, including the Dutch (E22Q), the Iowa (D23N), theDutch Iowa (E22Q, D23N), the Italian (E22K), and the Osaka (E22del)mutations and various embodiments are directed to synthetic Aβ peptideswith these amino acid substitutions that correspond to familial AD (seeFIGS. 3A-4B; Seq. ID Nos. 3-5, and 7) (I. Benilova, et al., 2012, citedsupra).

Although FIGS. 3A to 7B describe a number of modifications, it should beunderstood that various other modifications are possible that can reachthe same desired properties of solubility, stability of formedoligomers, prevention of uncontrolled aggregation, and ease of synthesisand fall with various embodiments of the invention. In addition, itshould be understood that a number embodiments of the synthetic Aβpeptides within the scope of the invention can incorporate differentsets of modifications. Some embodiments may only incorporate onemodification. Other embodiments may incorporate many, if not all,possible modifications. Thus, FIGS. 3A to 7B are merely representativeof the available modifications to achieve the desired properties.

Furthermore, synthetic Aβ peptides having substantially similarsequences are also to be covered. A substantially similar sequence is asequence having characteristics very similar to the original sequencesuch that the properties of β-sheet formation, trimer formation, higherorder oligomer formation, solubility, prevention of fibril-likeformation, and stability via cysteine disulfide bridges (if applicable),as those found in the original sequence are maintained. It is to beanticipated that synthetic cysteine-substituted Aβ peptides describedherein would be able to tolerate various alterations (e.g., an aminoacid substitution) and still maintain the properties of said Aβpeptides. In some embodiments, synthetic Aβ peptides may be altered byadding, removing, or substituting one amino acid. In more embodiments,peptides may be altered by adding, removing, or substituting two aminoacids. And in even more embodiments, peptides may be altered by adding,removing, or substituting three or more amino acids, assuming at leastsome of the properties of the original sequence are maintained. As it iswell known in the art, substitution of amino acids with similarqualities (e.g., hydrophobic for hydrophobic, hydrophilic forhydrophilic, acidic for acidic, basic for basic, etc.) are welltolerated and often have little effect on peptide properties.Accordingly, synthetic Aβ peptides may have substantial alterations andstill fall within the scope of peptides described herein.

In various embodiments, synthetic cysteine-substituted Aβ peptides withfurther modification can form covalently linked trimers. Variousembodiments are shown in FIGS. 5 and 6. In these embodiments, threemonomers of synthetic Aβ peptides can form trimers. Specifically, inthis embodiment, the formation of the trimers occurs when a disulfidebond is formed between C₁₇ of a first monomer and the C₂₁ of a secondmonomer. The same bond is repeated between the second monomer and athird, and again with the third monomer and the first. This trimerformation ensures a stable triangular-like shape that is resistant tofibril formation and uncontrolled aggregation. The further modificationscan also assist with trimer formation, dependent on various embodiments.For example, the N-methylation on various amino acids prevents monomerstacking and aggregation, thus promoting the monomers to form a trimerconformation. In addition, isosteric hydrophilic amino acid replacementincreases solubility monomers, which also promotes the formation ofoligomers and prevents insoluble fibril formation. The truncations canremove amino acids that are unnecessary for oligomer formation and the^(δ)Orn turn mimics ensure β-hairpin formation that promote stabilityand proper conformation of the oligomers. It should be noted, however,that the trimers in FIGS. 5 and 6 are not exhaustive of trimers, andthat specific modifications may be changed, removed, or duplicated andstill achieve the desired soluble oligomer formation. For example,crosslinked trimers can be formed using synthetic Aβ peptides having C₃₀and C₃₄ modifications.

Oligomers of the Synthetic Aβ Peptides

In several embodiments, the synthetic monomeric Aβ peptides canoligomerize to form higher-order tertiary conformations. Embodiments ofthese higher-order conformations include trimers, hexamers, dodecamers,and annular pores. Trimer embodiments are formulated from threemonomeric Aβ peptides and conforming into a triangular structure (FIG.8). Disulfide bridges that extend between cysteines of the monomericpeptides covalently link some embodiments of the trimer. Otherembodiments of the trimer may include further modifications of themonomeric peptides, which may help formulate and stabilize the trimers.

Trimers may be assembled using various Aβ peptides, in accordance with anumber embodiments. Crosslinked trimers require paired cysteinemodifications, such as C₁₇ and C₂₁ or C₃₀ and C₃₄, for example. Thecharacteristics of the trimer to be built depends on peptides andmodifications selected. Accordingly, peptides having variousmodifications can result in trimers having increased solubility,stability of formed oligomers, prevention of uncontrolled aggregation,and ease of synthesis.

More embodiments are directed to Aβ trimers that can further conforminto hexamers, dodecamers, and annular pores. Hexamer embodiments areformed from Aβ trimers that sandwich on top of one another (FIG. 9).Hydrophobic amino acids (e.g., F₁₉, I₃₂, L₃₄, and V₃₆) can formhydrophobic surfaces on a trimer, which can interact with otherhydrophobic surfaces of another trimer to conform into a stackedhexamer. The hexamers can further stack upon one another to form ahigher-order column. This mode of assembly is characteristic of certainAβ trimer embodiments.

Particular dodecamer embodiments are also formed by a hydrophobicstacking mechanism. Hydrophobic surfaces on four trimers can assemble ina tetrahedral fashion to conform into ball-shaped dodecamer (FIG. 10).Hydrogen bonds among the outer edges of the four trimers can stabilizethe dodecamer conformation. Furthermore, the hydrophobic surfaces of thefour trimers can line the inside of the dodecamer, creating a largehydrophobic cavity.

Further embodiments are direct to ball-shaped dodecamers capable ofpacking to form a crystal lattice. Within the crystal lattice, sixdodecamers can assemble to form annular pore like structures (FIG. 11).Hydrophobic surfaces displayed on the exterior of each dodecamer canstabilize these annular pore-like structures. At the interfaces betweenthe dodecamers in the annular pore, two trimers can pack to form asandwich-like hexamer. Each interface can be stabilized by hydrophobicpacking between the side chains of hydrophobic surfaces on each trimer.

Offset Synthetic Aβ Peptides

A number of embodiments are also directed to synthetic Aβ peptides withoffset β-strands. FIG. 12 provides a representation of an Aβ₁₇₋₃₆β-hairpin and a truncated mimic having canonical β-hairpin (Seq. ID Nos.12-14). In this peptide, the β-strands lineup such that the amides andcarboxyl groups form hydrogen between the following pairs of aminoacids: L₁₇ with V₃₆, F₁₉ with L₃₄, A₂₁ with I₃₂, and D₂₃ with A₃₀. Thiscanonical β-hairpin pairing, however, can be altered, as depicted inFIG. 13. In this noncanonical pairing, the β-strands lineup such thatthe amides and carboxyl groups form hydrogen between the following pairsof amino acids: K₁₆ with V₃₆, V₁₈ with L₃₄, F₂₀ with I₃₂, and E₂₂ withA₃₀.

In several embodiments, offset Aβ β-hairpins are truncated and a ^(δ)Ornis inserted into amino acid position 15 to covalently link amino acid 15with the C-terminus of amino acid 36, effectively eliminating the nativeC and N-termini (FIG. 13; Seq. ID Nos. 15-17). In addition, otherembodiments have a ^(δ)Orn inserted into amino acid position 29 tocovalently link amino acid 29 with the C-terminus of amino acid 22,effectively eliminating the amino acids 23 to 29 (FIG. 13).

Embodiments are also directed to substitution of alkyl (e.g., methyl),aryl (e.g., benzyl, nitrobenzyl) or other similarly bulky groups with anH on one of the amides of a central amino acid having an outward-facingamide that is not involved in β-hairpin hydrogen bonding (see FIGS. 12and 13). The bulky group can be substituted on either β-strand, butshould not interfere with trimer formation. As shown in FIG. 12, aminoacids F₂₀ and G₃₃ are ideal candidates for N-methylation in accordancewith a number of embodiments for the Aβ₁₇₋₃₆ β-hairpin. Likewise, aminoacids F₁₉ and G₃₃ are ideal candidates for N-methylation in accordancewith a number of embodiments for the offset Aβ β-hairpin (FIG. 13). Theaddition of bulky groups to the peptide backbone sterically hinders theinteraction and stacking of β-strands and thus prevents uncontrolledaggregation of Aβ peptides into fibrils.

More embodiments are directed to replacement of hydrophobic amino acidswith hydrophilic amino acids, and more specifically to isosterichydrophilic amino acid replacements. For example, a methionine can beoxidized to or substituted with ornithine, methionine sulfoxide ormethionine sulfone (e.g., Met₃₅→Orn₃₅, Met₃₅→MetO₃₅) (see FIGS. 12 and13).

Many embodiments are directed to synthetic Aβ peptides that reflectfamilial AD peptides. In particular, synthetic Aβ peptide embodimentsincorporate familial mutations that occur within the β-hairpin region ofthe peptide. Many mutations are known to occur within this region,including the Dutch (E22Q), the Iowa (D23N), the Dutch Iowa (E22Q,D23N), the Italian (E22K), and the Osaka (E22del) mutations and variousembodiments are directed to synthetic Aβ peptides with these amino acidsubstitutions that mimic familial AD (see FIGS. 12 and 13).

Although FIGS. 12 and 13 describe a number of modifications, it shouldbe understood that various other modifications are possible that canreach the same desired characteristics of solubility, stability offormed oligomers, prevention of uncontrolled aggregation, and ease ofsynthesis and fall with various embodiments of the invention. Inaddition, it should be understood that a number embodiments of thesynthetic Aβ peptides within the scope of the invention can incorporatedifferent sets of modifications. Some embodiments may only incorporateone modification. Other embodiments may incorporate many, if not all,possible modifications. Thus, FIGS. 12 and 13 are merely representativeof the available modifications to achieve the desired properties.

Furthermore, synthetic Aβ peptides having substantially similarsequences are also to be covered. A substantially similar sequence is asequence having characteristics very similar to the original sequencesuch that the properties of β-sheet formation, trimer formation, higherorder oligomer formation, solubility, prevention of fibril-likeformation, and stability, as those found in the original sequence aremaintained. It is to be anticipated that synthetic offset Aβ peptidesdescribed herein would be able to tolerate various alterations (e.g., anamino acid substitution) and still maintain the properties of said Aβpeptides. In some embodiments, synthetic Aβ peptides may be altered byadding, removing, or substituting one amino acid. In more embodiments,peptides may be altered by adding, removing, or substituting two aminoacids. And in even more embodiments, peptides may be altered by adding,removing, or substituting three or more amino acids, assuming at leastsome of the properties of the original sequence are maintained. As it iswell known in the art, substitution of amino acids with similarqualities (e.g., hydrophobic for hydrophobic, hydrophilic forhydrophilic, acidic for acidic, basic for basic, etc.) are welltolerated and often have little effect on peptide properties.Accordingly, synthetic Aβ peptides may have substantial alterations andstill fall within the scope of peptides described herein.

Applications of Synthetic Aβ Peptides

Several embodiments are directed to applications and uses of syntheticAβ peptides and oligomers, including various embodiments directed totoxicological administration, antigen binding molecule development, andsmall molecule development. In several embodiments, synthetic Aβpeptides and oligomers are cytotoxic and can cause cell death,apoptosis, necrosis, autophagy, or any combination thereof. In morespecific embodiments, the peptides and oligomers are especially toxic toneurons and other neuronal cells. Other embodiments are directed to theability of peptides and oligomers to stimulate cellular lactatedehydrogenase (LDH) release or caspase-3 induction.

A number of embodiments are also directed to antigen binding moleculedevelopment using immunogenic cocktails having synthetic Aβ peptides andoligomers. Several of these embodiments utilize Aβ peptides andoligomers as antigens, with or without adjuvant, to produce antibodiesin an immunocompetent animal, such as human, rabbit, goat, mouse, rat,chicken, guinea pig, or any other suitable species. Further embodimentsinclude development of monoclonal antibodies that recognize synthetic Aβpeptides and oligomers. Other embodiments are directed to developedantigen binding molecules that specifically recognize Aβ oligomers butnot Aβ monomers.

Various embodiments are also directed to the development of smallmolecules (e.g., dyes) capable of interacting with synthetic Aβ peptidesand oligomers. In many embodiments, the small molecules are able toelicit a response when in contact, or in the vicinity, of Aβ peptides oroligomers. Some embodiments are small molecule probes that are able todetect Aβ peptides and oligomers by a suitable method (e.g. fluorescencemicroscopy, positron emission tomography (PET)). More particularembodiments the small molecule probes detect Aβ oligomers but notmonomers. Other embodiments are small molecule drugs capable of reducingthe toxic effects of Aβ peptides and oligomers.

Antigen Binding Molecule Development & Purification

In accordance with a number of embodiments, antigen binding molecules(e.g., antibodies) can be developed with high specificity, preferenceand affinity for soluble oligomeric Aβ, but not monomer or insolublefibrils. In many of these embodiments, the high affinity oligomerantigen binding molecules are developed using synthetic Aβ trimers, suchas those described herein. Embodiments are also directed to the use ofsynthetic Aβ trimers to select and/or purify antigen binding molecules,as determined by their specificity, preference, and affinity to Aβoligomers.

Antigen binding molecules are to be any antibodies, fragments ofantibodies, variants, and derivatives thereof capable of specificallybinding an antigen. These include, but are not limited to, polyclonal,monoclonal, multispecific, human, humanized, primatized, or chimericantibodies, single chain antibodies, epitope-binding fragments, e.g.,Fab, Fab′ and F(ab′)₂, Fd, Fvs, single-chain Fvs (scFv), single-chainantibodies, disulfide-linked Fvs (sdFv), fragments comprising either aVL or VH domain, and fragments produced by a Fab expression library.

By “specifically binds,” or “specifically recognizes,” usedinterchangeably herein, it is generally meant that an antigen bindingmolecule (e.g., an antibody binds to an epitope via its antigen bindingdomain) and that the binding entails some complementarity between theantigen binding domain and the epitope. According to this definition, anantibody is said to “specifically bind” to an epitope when it binds tothat epitope, via its antigen binding domain more readily than it wouldbind to a random, unrelated epitope.

By “preferentially binds,” it is meant that an antigen binding molecule(e.g., antibody) specifically binds to an epitope more readily than itwould bind to a related, similar, homologous, or analogous epitope.Thus, an antibody that “preferentially binds” to a given epitope wouldmore likely bind to that epitope than to a related epitope, even thoughsuch an antibody may cross-react with the related epitope.

As used herein, the term “affinity” refers to a measure of the strengthof the binding of an individual epitope by the antigen binding molecule.

Antibodies are composed of a light chain and heavy chain. In general,the light and heavy chains are covalently bonded to each other, and the“tail” portions of the two heavy chains are typically bonded to eachother by covalent disulfide linkages. Non-covalent linkages between twoheavy chains can be used, however, as is typical when the antibodies aregenerated in culture.

Both the light and heavy chains are divided into regions of structuraland functional homology, such as the constant and variable domains. Thevariable domains of both the light (VL) and heavy (VH) chain portionsdetermine antigen recognition and specificity. Conversely, the constantdomains of the light chain (CL) and the heavy chain (CH1, CH2 or CH3)confer important biological properties such as secretion, transplacentalmobility, Fe receptor binding, complement binding, etc.

The antigen recognition of the VL and VH domains is determined by thecomplementarity determining regions (CDRs). In naturally occurringantibodies, there are six CDRs, which are short, non-contiguoussequences that are specifically positioned to form the antigen bindingdomain. The antigen binding domain formed by the positioned CDRs definesa surface complementary to the epitope on the innnunoreactive antigen.This complementary surface promotes the non-covalent binding of theantibody to its cognate epitope. The amino acids comprising the CDRs andthe framework regions, respectively, can be readily identified for anygiven heavy or light chain variable region by one of ordinary skill inthe art, since they have been precisely defined (see, Chothia and Lesk,J. Mol. Biol. 1987 196, 901-917, which is incorporated herein byreference).

Antibody Acquisition by Immunization

An embodiment for the production of antibodies with high affinity forsoluble Aβ oligomers is depicted in FIG. 14. Process 1400 begins with anacquisition of soluble Aβ trimers (1401). Ideally, Aβ trimers would formstable oligomers and not aggregate and form fibrils, such as thesynthetic Aβ trimers described herein. The specific Aβ trimer to be usedwould likely depend on the result desired. For example, antibodies couldbe generated with high affinity for Aβ oligomers having specificfamilial AD mutations.

Process 1400 continues with administering immunocompetent animals withan immunogenic cocktail having soluble Aβ trimers (1403). Anyimmunocompetent animal can be used, such as, for example, human, rabbit,goat, mouse, rat, chicken, or guinea pig. Immunocompetent animals can beadministered with a stimulating amount of with soluble Aβ trimer, withor without conjugate and with or without adjuvant. A stimulating amountof soluble Aβ trimer is the amount required to stimulate an immuneresponse that results in production of a collectable amount ofantibodies that have affinity for soluble Aβ oligomers. The stimulatingamount may also depend on the use of conjugate and/or adjuvant. Anyappropriate conjugate can be used, such as, for example, hemocyanin.Likewise, any appropriate adjuvant can be used, such as, for example,complete Freund's adjuvant.

Injection of soluble Aβ trimers into an immunocompetent animal can beoptionally repeated multiple (1405). Often, repeat administrations canimprove antibody production. The appropriate amount of administrationsdepends on the application, however, typically one, two, three, or fouradministrations are performed.

Sera, plasma, blood, and/or other hematopoietic tissue having highaffinity antibodies and/or antibody generating cells are harvested fromimmunocompetent animals an appropriate amount of time after the finaladministration of soluble Aβ trimer (1407). The appropriate amount oftime is the time required for the immunocompetent animal to have animmune response and generate antibodies, which is dependent in part onthe immunocompetent animal used. For example, an appropriate time toharvest antibodies from rabbits is typically around 30 days after lastimmunization. Harvesting of sera, plasma and/or blood can be performedby any of the many methods known in the art.

Once sera, plasma, blood and/or hematopoietic tissue having highaffinity antibodies cells are harvested, antibodies may be used in theirnatural buffer or further purified by a number of methods in accordanceof a number of embodiments. Likewise, antibody generating cells may becultured and/or stored in accordance with several embodiments.

Oligomer Aβ Vaccination

A number of embodiments utilize methods for preventing or amelioratingAlzheimer's disease. Accordingly, various embodiments contemplateadministering to individuals immunogenic compositions, proposed to besuitable for use as a vaccine, prepared using soluble Aβ peptides,trimers and higher order oligomers, as described herein. In otherembodiments Aβ compositions can be used in combination with othersecreted virulence proteins, surface proteins or immunogenic fragmentsthereof. In certain aspects, antigenic material is extensively dialyzedto remove undesired small molecular weight molecules and/or lyophilizedfor more ready formulation into a desired vehicle.

The preparation of vaccines that contain polypeptide or peptidesequence(s) as active ingredients is generally well understood in theart, as exemplified by U.S. Pat. Nos. 4,608,251; 4,601,903; 4,599,231;4,599,230; and 4,596,792; each of which is incorporated herein byreference. Typically, such vaccines are prepared as injectables eitheras liquid solutions or suspensions: solid forms suitable for solution inor suspension in liquid prior to injection may also be prepared. Thepreparation may also be emulsified. The active immunogenic ingredient isoften mixed with excipients that are pharmaceutically acceptable andcompatible with the active ingredient. Suitable excipients are, forexample, water, saline, dextrose, glycerol, ethanol, or the like andcombinations thereof. In addition, if desired, the vaccine may containamounts of auxiliary substances such as wetting or emulsifying agents,pH buffering agents, or adjuvants that enhance the effectiveness of thevaccines. In specific embodiments, vaccines are formulated with acombination of substances, as described in U.S. Pat. Nos. 6,793,923 and6,733,754, each of which is incorporated herein by reference.

Vaccines may be conventionally administered parenterally, by injection,for example, either subcutaneously or intramuscularly. Additionalformulations which are suitable for other modes of administrationinclude suppositories and, in some cases, oral formulations. Forsuppositories, traditional binders and carriers may include, forexample, polyalkalene glycols or triglycerides: such suppositories maybe formed from mixtures containing the active ingredient in the range ofabout 0.5% to about 10%, preferably about 1% to about 2%. Oralformulations include such normally employed excipients as, for example,pharmaceutical grades of mannitol, lactose, starch, magnesium stearate,sodium saccharine, cellulose, magnesium carbonate and the like. Thesecompositions take the form of solutions, suspensions, tablets, pills,capsules, sustained release formulations or powders and contain about10% to about 95% of active ingredient, preferably about 25% to about70%.

Vaccine compositions would normally be administered as pharmaceuticallyacceptable compositions that include physiologically acceptablecarriers, buffers or other excipients. As used herein, the term“pharmaceutically acceptable” refers to those compounds, materials,compositions, and/or dosage forms which are, within the scope of soundmedical judgment, suitable for contact with the tissues of human beingsand animals without excessive toxicity, irritation, allergic response,or other problem complications commensurate with a reasonablebenefit/risk ratio. The term “pharmaceutically acceptable carrier,”means a pharmaceutically acceptable material, composition or vehicle,such as a liquid or solid filler, diluent, excipient, solvent orencapsulating material, involved in carrying or transporting a chemicalagent.

An effective amount of therapeutic or prophylactic composition isdetermined based on the intended goal. The term “unit dose” or “dosage”refers to physically discrete units suitable for use in a subject, eachunit containing a predetermined quantity of the composition calculatedto produce the desired responses discussed above in association with itsadministration, i.e., the appropriate route and regimen. The quantity tobe administered, both according to number of treatments and unit dose,depends on the protection desired.

Precise amounts of the composition also depend on the judgment of thepractitioner and are peculiar to each individual. Factors affecting doseinclude physical and clinical state of the subject, route ofadministration, intended goal of treatment (alleviation of symptomsversus cure), and potency, stability, and toxicity of the particularcomposition.

Typically, vaccines are administered in a manner compatible with thedosage formulation, and in such amount as will be therapeuticallyeffective and immunogenic. The quantity to be administered depends onthe subject to be treated, including the capacity of the individual'simmune system to synthesize antibodies and the degree of protectiondesired. Precise amounts of active ingredient required to beadministered depend on the judgment of the practitioner. However,suitable dosage ranges are of the order of several hundred micrograms ofactive ingredient per vaccination. Suitable regimes for initialadministration and booster shots are also variable, but are typified byan initial administration followed by subsequent inoculations or otheradministrations.

Upon formulation, solutions will be administered in a manner compatiblewith the dosage formulation and in such amount as is therapeutically orprophylactically effective. The formulations are easily administered ina variety of dosage forms, such as the type of injectable solutionsdescribed within.

The manner of application may be varied widely. Any of the conventionalmethods for administration of a vaccine are applicable. These arebelieved to include oral application within a solid physiologicallyacceptable base or in a physiologically acceptable dispersion,parenterally, by injection and the like. The dosage of the vaccine willdepend on the route of administration and will vary according to thesize and health of the subject.

In certain instances, it will be desirable to have multipleadministrations of the vaccine, e.g., 2, 3, 4, 5, 6 or moreadministrations. The vaccinations can be at 1, 2, 3, 4, 5, 6, 7, 8, to5, 6, 7, 8, 9, 10, 11, 12 twelve week intervals, including all rangesthere between. Periodic boosters at intervals of 1-5 years will bedesirable to maintain protective levels of the antibodies. The course ofthe immunization may be followed by assays for antibodies against theantigens, as described in U.S. Pat. Nos. 3,791,932; 4,174,384 and3,949,064, each of which is incorporated herein by reference.

A given composition may vary in its immunogenicity. It is oftennecessary therefore to boost the host immune system, as may be achievedby coupling a peptide or polypeptide to a carrier. Exemplary andpreferred carriers are keyhole limpet hemocyanin (KLH) and bovine serumalbumin (BSA). Other albumins such as ovalbumin, mouse serum albumin, orrabbit serum albumin can also be used as carriers. Means for conjugatinga polypeptide to a carrier protein are well known in the art and includeglutaraldehyde, m-maleimidobencoyl-N-hydroxysuccinimide ester,carbodiimyde, and bis-biazotized benzidine.

The immunogenicity of polypeptide or peptide compositions can beenhanced by the use of non-specific stimulators of the immune response,known as adjuvants. Suitable adjuvants include all acceptableimmunostimulatory compounds, such as cytokines, toxins, or syntheticcompositions. A number of adjuvants can be used to enhance an antibodyresponse against Aβ peptides, trimers and higher order oligomers.Adjuvants can (1) trap the antigen in the body to cause a slow release;(2) attract cells involved in the immune response to the site ofadministration; (3) induce proliferation or activation of immune systemcells; or (4) improve the spread of the antigen throughout the subject'sbody.

Adjuvants include, but are not limited to, oil-in-water emulsions,water-in-oil emulsions, mineral salts, polynucleotides, and naturalsubstances. Specific adjuvants that may be used include IL-1, IL-2,IL-4, IL-7, IL-12, γ-interferon, GMCSP, BCG, aluminum salts, such asaluminum hydroxide or other aluminum compound, MDP compounds, such asthur-MDP and nor-MDP, CGP (MTP-PE), lipid A, and monophosphoryl lipid A(MPL). RIBI, which contains three components extracted from bacteria,MPL, trehalose dimycolate (TDM), and cell wall skeleton (CWS) in a 2%squalene/Tween 80 emulsion. MHC antigens may even be used. Othersadjuvants or methods are exemplified in U.S. Pat. Nos. 6,814,971,5,084,269, 6,656,462, each of which is incorporated herein by reference.

Various methods of achieving adjuvant affect for the vaccine includesuse of agents such as aluminum hydroxide or phosphate (alum), commonlyused as about 0.05 to about 0.1% solution in phosphate buffered saline,admixture with synthetic polymers of sugars (Carbopol®) used as an about0.25% solution, aggregation of the protein in the vaccine by heattreatment with temperatures ranging between about 70° to about 101° C.for a 30-second to 2-minute period, respectively. Aggregation byreactivating with pepsin-treated (Fab) antibodies to albumin; mixturewith bacterial cells (e.g., C. parvum), endotoxins or lipopolysaccharidecomponents of Gram-negative bacteria; emulsion in physiologicallyacceptable oil vehicles (e.g., mannide mono-oleate (Aracel A)); oremulsion with a 20% solution of a perfluorocarbon (Fluosol-DA®) used asa block substitute may also be employed to produce an adjuvant effect.

Examples of adjuvants include complete Freund's adjuvant (a non-specificstimulator of the immune response containing killed Mycobacteriumtuberculosis), incomplete Freund's adjuvants, and aluminum hydroxide.

Administration of the immunogenic compositions, in accordance withnumerous embodiments, to a patient/subject will follow general protocolsfor the administration of such compounds, taking into account thetoxicity, if any, of the synthetic Aβ peptide/oligomer composition, orother compositions described herein. It is expected that the treatmentcycles would be repeated as necessary. It also is contemplated thatvarious standard therapies, such as hydration, may be applied incombination with the described therapy.

Soluble synthetic Aβ peptides and oligomers can be formulated forparenteral administration (e.g., formulated for injection via theintravenous, intramuscular, subcutaneous, or even intraperitonealroutes). The preparation of an aqueous composition that contains acompound or compounds that increase the expression of an MHC class Imolecule will be known to those of skill in the art in light of thepresent disclosure. Typically, such compositions can be prepared asinjectables, either as liquid solutions or suspensions; solid formssuitable for use to prepare solutions or suspensions upon the additionof a liquid prior to injection can also be prepared; and, thepreparations can also be emulsified.

Solutions of soluble synthetic Aβ peptides and oligomers can be preparedin water suitably and can be mixed with a surfactant, if necessary.Dispersions can also be prepared in glycerol, liquid polyethyleneglycols, and mixtures thereof and in oils. Under ordinary conditions ofstorage and use, these preparations contain a preservative to preventthe growth of microorganisms.

Sterile injectable solutions can be prepared by incorporating thesoluble synthetic Aβ peptides and oligomers in the required amount inthe appropriate solvent with various of the other ingredients enumeratedabove, as required, followed by filtered sterilization. Generally,dispersions are prepared by incorporating the various sterilized activeingredients into a sterile vehicle which contains the basic dispersionmedium and the required other ingredients from those enumerated above.

Antibody Acquisition from Human Patients

Antibodies and antibody generating cells can also be identified acquiredfrom other sources in addition to immunized animals. For example,antibodies and antibody generating cells can be acquired from anunimmunized human subject. It is possible to identify an antibody orantibody-producing cell from specific collectives or healthy subjects,preselected by clinical criteria (e.g., age, cognitive ability,propensity for AD), without prerecognition of a target structure epitope(e.g., soluble Aβ oligomers). Once a subject is identified, B cells andB memory cells can be collected and tested for their production ofantibodies having high specificity, preference, and affinity.

In one particular embodiment, it may be ideal to source antibodyproducing cells of an aging individual not having cognitive defects orclinical signs of dementia. In this embodiment, the sample is obtainedfrom subject having the following criteria: a) being 65, preferably 70and more preferably 75 years of age or older; b) having full cognitivecapacity and good health; and c) having no clinical signs of dementia orhaving unusually slow rates of progression of disease despite thepresence of an established clinical diagnosis of probable Alzheimer'sdisease or having unusually low conversion rates from Mild CognitiveImpairment (MCI) to full blown Alzheimer's disease.

In another embodiment, samples may be obtained from the selectedindividuals by a) purifying B cells or B memory cells from a samplewhich has been identified to contain antibodies which preferentiallybind to soluble Aβ trimers but not or with significantly lower affinityto monomers and/or insoluble fibrils; b) obtaining the immunoglobulingene repertoire encoding said antibodies from said B cells or B memorycells; and c) using said repertoire to express at least one of saidantibodies in a recombinant system. In various embodiments, theimmunoglobulin gene repertoire may be determined by sequencing the mRNAor DNA by a number of known methods practiced in the field.

There are a number of known methods to produce clones of immortalizedhuman B cell and B memory lymphocyte colonies, such as, for exampleusing Epstein Barr Virus in the presence of a polyclonal B cellactivator or construction of human hybridomas. Antibodies may becontinually produced using an immortalized human B cell line andharvested and purified by methods known in the art.

Antigen binding molecules may also be continually produced byrecombinant expression in a production cell line. Genetic material canbe created using the appropriate immunoglobulin cDNA representing theantibody to be expressed. The coding sequences, at a minimum, shouldinclude the variable regions that provide the antigen binding ability.The genetic information can be inserted into a vector, which can betransfected in to standard recombinant host cells. A number ofrecombinant host cells are known in the art, including, but not limitedto CHO cells, HEK 293 cells, and HeLa cells. Antigen binding moleculesmay be harvested and purified from the production cells by methods knownin the art.

Monoclonal Antibody Development

Monoclonal antibodies can be prepared using a wide variety of techniquesknown in the art including the use of hybridoma, recombinant, and phagedisplay technologies, or a combination thereof. For example, monoclonalantibodies can be produced using hybridoma techniques including thoseknown in the art and taught, for example, in Harlow et al., Antibodies:A Laboratory Manual, Cold Spring Harbor Laboratory Press, 2nd ed. 1988,the disclosure of which is incorporated herein by reference. The term“monoclonal antibody” refers to an antibody that is derived from asingle clone, including any eukaryotic, prokaryotic, or phage clone, andnot the method by which it is produced. Thus, the term “monoclonalantibody” is not limited to antibodies produced through hybridomatechnology. In certain embodiments, antibodies of the present inventionare derived from human B cells that have been immortalized viatransformation.

In the well-known hybridoma process (Kohler et al., Nature 1975 256,495; the disclosure of which is incorporated herein by reference) therelatively short-lived, or mortal, lymphocytes from a mammal (e.g., Bcells derived from a human subject as described herein) are fused withan immortal tumor cell line (e.g., a myeloma cell line), thus, producinghybrid cells or “hybridomas” which are both immortal and capable ofproducing the genetically coded antibody of the B cell. The resultinghybrids are segregated into single genetic strains by selection,dilution, and regrowth with each individual strain comprising specificgenes for the formation of a single antibody. Each single strainproduces antibodies, which are homogeneous against a desired antigen.

Hybridoma cells thus prepared are seeded and grown in a suitable culturemedium that preferably contains one or more substances that inhibit thegrowth or survival of the unfused, parental myeloma cells. Those skilledin the art will appreciate that reagents, cell lines and media for theformation, selection and growth of hybridomas are commercially availablefrom a number of sources and standardized protocols are wellestablished. Generally, culture medium in which the hybridoma cells aregrowing is assayed for production of monoclonal antibodies against thedesired antigen (e.g., soluble Aβ oligomers). The binding specificity ofthe monoclonal antibodies produced by hybridoma cells is determined byin vitro assays such as immunoprecipitation, radioimmunoassay (RIA), orenzyme-linked immunosorbent assay (ELISA). After hybridoma cells areidentified that produce antibodies of the desired specificity, affinityand/or activity, the clones may be subcloned by limiting dilutionprocedures and grown by standard methods (Goding, Monoclonal Antibodies:Principles and Practice, Academic Press, 1986 pp 59-103)). It willfurther be appreciated that the monoclonal antibodies secreted by thesubclones may be separated from culture medium, ascites fluid or serumby conventional purification procedures such as, for example, protein-A,hydroxylapatite chromatography, gel electrophoresis, dialysis oraffinity chromatography.

Selection and Purification of Soluble Aβ Oligomer Binding Molecule

Embodiments are also directed to the selection of antigen bindingmolecules having high specificity, preference, and affinity for solubleAβ oligomers. In this embodiment, soluble Aβ trimers, such as thosedescribed herein, are used to identify and select such antigen bindingmolecules. Soluble Aβ binding molecules can be used for a varietydownstream applications, including, but not limited to, diagnosis andtreatment of Aβ related diseases (e.g., AD).

Embodiments can begin with acquisition of antigen binding molecules.Antigen binding molecules can be obtained in a variety of methods,including those described herein. Once antigen binding molecules areobtained, they can be screened for their specificity, preference, andaffinity for soluble Aβ oligomers using soluble Aβ trimers). Preferably,highly stable, crosslinked trimers that do not form fibrils are used,such as those described herein.

Many assays are known in the art to screen the specificity of antibodiesfor a particular antigen. These assays include, but are not limited to,Western blot, immunoprecipitation, RIA, and ELISA. Accordingly, highlystable, crosslinked trimers that do not form fibrils can be used asantigens in these assays to determine their specificity to soluble Aβoligomers.

A number of assays are also known to determine antibody preference for aparticular antigen over a similar antigen. Particularly, in thisapplication, antigen binding molecules that preferentially bind solubleAβ oligomers with low cross-reactivity with monomers and insolublefibrils is desired. Accordingly, specificity assays, such as thosedescribed above, can be used to directly compare antigen bindingmolecules' ability to bind soluble Aβ oligomers, monomers, and insolublefibrils. In addition to comparison assays, direct competition assays canbe performed, wherein antigen binding molecules are in contact withsoluble Aβ oligomers, monomers, and insoluble fibrils and theirpreference for each antigen is determined.

Binding affinities of antigen binding molecules can be measured by anumber of assays. In many of these assays, the dissociation constant(Kd) can be measured directly. Alternatively, affinity can be determinedqualitatively by a number assays, including, but not limited to Westernblot, immunoprecipitation, RIA, and ELISA.

Soluble Aβ trimers can also be used to purify solutions of antigenbinding molecules, such as those derived from the methods describedherein. Accordingly, antibodies may be derived from animal hematopoietictissue (e.g., sera, plasma, blood) or from tissue culture (e.g.,hybridoma, immortalized B-cell lines). These antigen binding cells maybe a purified from a variety of known purification procedures such as,for example, protein-A, hydroxylapatite chromatography, gelelectrophoresis, dialysis or affinity chromatography. In particular,soluble Aβ oligomer binding molecules can be specifically purified usingsoluble Aβ trimers via affinity chromatography.

Affinity chromatography is a method of separating biochemical mixturesbased on highly specific interaction between antigen and antibody.Accordingly, soluble Aβ trimers, such as those described herein, can befixed to matrix (e.g., agarose) to create a solid support. Often, thesolid support is packed into a column, but alternative methods are alsoacceptable (e.g., slurry centrifugation techniques). Antibody containingsolutions can be optionally mixed with binding solutions (e.g.,phosphate buffered saline (PBS)) before being passed through the solidphase, wherein the highly specific antibodies are captured by the fixedsoluble Aβ trimers. Once the antibody containing solution passesthrough, the solid support can be washed with an appropriate buffer(e.g. PBS) multiple times to clear all non-binding molecules. Oncewashed, the antibodies can be eluted using a suitable buffer (e.g., 0.1M glycine-HCl, pH 2.5-30) that will dissociate the antibody from thesoluble Aβ trimers. Once pure, the elution buffer can be neutralized, ifnecessary, and/or exchanged with an appropriate storage or applicationbuffer.

Affinity chromatography can also be used to remove cross-reactiveantibodies that have are reactive to undesired antigens, such as Aβmonomers and insoluble fibrils. Accordingly, Aβ monomers and insolublefibrils can be fixed to a matrix to create a solid support. Antibodysolutions can be passed through the solid support, wherein antibodiesspecific to these antigens will bind. The unbound antibodies can bepassed through in a neutral buffer (e.g., PBS). The elute containingsoluble Aβ oligomer antibodies can either be stored, or then processedthrough the previously described affinity chromatography method withsoluble Aβ trimers fixed to a solid support to further purify theantibody solution.

EXEMPLARY EMBODIMENTS

Biological and chemical data support the aforementioned synthetic Aβpeptides and oligomers in variety embodiments as described. The datademonstrate that Aβ peptides can be synthesized with variousmodifications that are capable of supramolecular assembly. X-raycrystallography confirms the peptide conformations, intramolecularinteraction, and higher-order oligomerization. Analytical reverse-phasehigh performance liquid chromatography (RP-HPLC) establishes that thedescribed methods yield high levels of Aβ oligomers that are capable ofeven higher ordered structures. Biochemical assays reveal that syntheticAβ peptides and oligomers are cytotoxic and capable of antibodyproduction and detection.

Aβ Peptides Capable of Crosslinked Trimerization

Previous studies have identified and elucidated hitherto undiscoveredmodes of supramolecular assembly of macrocyclic β-sheet peptides derivedfrom amyloidogenic peptides and proteins (R. K. Spencer, et al., J. Am.Chem. Soc. 2014 136, 5595-5598; R. K. Spencer, et al., J. Am. Chem. Soc.2015 137, 6304-6311; P. J. Salveson, et al., J. Am. Chem. Soc. 2016 138,4458-4467; the disclosures of which are incorporated herein byreference). These studies reported X-ray crystallographic structures oftwo homologous trimers formed by two macrocyclic β-sheet peptidesderived from Aβ₁₇₋₃₆. These peptides—peptides 1 and 2—contain Aβ₁₇₋₂₃and Aβ₃₀₋₃₆ β-strands covalently linked by two δ-linked ornithine(^(δ)Orn) turn mimics (FIGS. 15A and 15B; Seq. ID Nos. 18-21). The δOrnthat connects residues D₂₃ and A₃₀ replaces the Aβ₂₄₋₂₉ loop; the δOrnthat connects residues L₁₇ and V₃₆ reinforces β-sheet structure.Ornithine (α-linked) was included as a hydrophilic isostere ofmethionine at position 35 to improve the solubility of the peptides.Peptides 1 and 2 both contain an N-methyl group to block uncontrolledaggregation: peptide contains an N-methyl group on G₃₃; peptide 2contains an N-methyl group on F₂₀.

X-ray crystallography revealed that peptides 1 and 2 fold to formβ-hairpins that assemble to form oligomers. In the X-raycrystallographic structures of peptides 1 and 2, three β-hairpinsassemble in a triangular fashion to form trimers, which are stabilizedby hydrogen bonding and hydrophobic interactions between monomers (FIGS.16A and 16B). At the three corners of each trimer, the main chain ofresidue V₁₈ on one macrocyclic β-sheet hydrogen bonds with the mainchain of residue E₂₂ on the adjacent macrocyclic β-sheet. Clusteringbetween hydrophobic residues at the corners of each trimer providesadditional stability. In the crystal lattice, the trimers furtherassemble to form hexamers and dodecamers. The trimers, hexamers, anddodecamers formed by peptide 1 are morphologically identical to thetrimers, hexamers, and dodecamers formed by peptide 2. The oligomersformed by peptides 1 and 2, however, are labile and dynamic in aqueoussolution, making it difficult to correlate their biological andbiophysical properties with their structures. Stabilization of Aβoligomers would help overcome these complications.

Aβ Peptides Capable of Stable Trimerization with Covalent DisulfideLinkage

Design and Synthesis of Peptides 3 and 4 and Trimers 3 and 4.

The structures of the trimers formed by peptides 1 and 2 could beimproved if the trimers could be further stabilized. To try to stabilizethe trimers, amino acid residues L₁₇ and A₂₁ were replaced with cysteineresidues that possibly could allow crosslinking the peptides to formcovalent trimers containing three disulfide linkages (see FIGS. 17A and17B; Seq. ID Nos. 22-25). It was predicted that the cysteinesubstitutions would be tolerated because the resulting C₁₇-C₂₁crosslinks would be near isosteric with L₁₇ and A₂₁, maintaining asimilar level of hydrophobicity and would not alter the charge of thetrimer.

Peptides 3 and 4 were synthesized by similar procedures to thosedeveloped for other macrocyclic peptides: synthesis of the correspondinglinear peptide on 2-chlorotrityl resin, followed by cleavage of theprotected linear peptide from the resin, solution-phasemacrolactamization, and global deprotection of the resulting macrocyclicpeptide (See, R. K. Spencer, et al., J. Am. Chem. Soc. 2014 136,5595-5598; R. K Spencer, et al., J. Am. Chem. Soc. 2015 137, 6304-6311;P. J. Salveson, et al., J. Am. Chem. Soc. 2016 138, 4458-4467; citedsupra). Peptides 3 and 4 were purified by reverse-phase HPLC (RP-HPLC)followed by lyophilization of pure fractions. Typical syntheses on a 0.1mmol scale afforded ˜55 mg of peptides 3 and 4 in ≥95% purity. Highpurity of peptides 3 and 4 minimized off-target products in thesubsequent oxidation reactions.

It was anticipated that oxidation of peptides 3 and 4 to form trimerswould be challenging. The peptides have the potential to form complexmixtures of monomeric, dimeric, trimeric, and higher oligomericoxidation products. Five different oxidation products of trimer size orsmaller are possible in the oxidation reactions of peptides 3 and 4: (1)a monomer that contains an intramolecular disulfide bond between C₁₇ andC₂₁, (2) an antiparallel bis-disulfide crosslinked dimer, (3) a parallelbis-disulfide crosslinked dimer, (4) an asymmetric tris-disulfidecrosslinked trimer, and (5) a symmetric tris-disulfide crosslinkedtrimer (FIG. 18). The desired trimers 3 and 4 are symmetrictris-disulfide crosslinked trimers (FIGS. 19A and 19B).

A two-step procedure was developed for preparing trimers 3 and 4 frompeptides 3 and 4. In the first step, peptides 3 and 4 were allowed tooxidize at relatively high concentration of peptide (6 mM) in 20% (v/v)aqueous DMSO for 48 h. In the second step, the reaction mixture wasdiluted with water to a low concentration (˜250 μM) and the oxidizedpeptides were allowed to equilibrate over 48 h. Through this procedure,peptides 3 and 4 crosslink to form substantial amounts of the desiredsymmetric crosslinked trimers 3 and 4. In the oxidation reaction ofpeptide 3 three major products were observed—timer 3, a crosslinkeddimer, and the disulfide monomer (FIG. 20A). In the oxidation reactionof peptides 4, two major products were observed—timer 4 and thedisulfide monomer, but not appreciable amounts of either possiblecrosslinked dimer (FIG. 20B). Trimers 3 and 4 were purified by RP-HPLCfollowed by lyophilization of pure fractions to yield ˜15 mg of trimer 3and ˜25 mg of trimer 4—each with ≥95% purity—from a 0.1 mmol scalesynthesis of peptides 3 and 4.

X-Ray Crystallographic Structure Determination of Trimers 3 and 4.

The structures of trimers 3 and 4 were elucidated by X-raycrystallography. One of the challenges in X-ray crystallography isdetermining the X-ray crystallographic phases. Doing so often requiresincorporation of a heavy atom—such as selenium, bromine oriodine—through covalent modification. In previously solving the X-raycrystallographic structures of peptides 1 and 2, homologues wereprepared containing p-iodophenylalanine. In solving the X-raycrystallographic structures of trimers 3 and 4, two techniques for X-raycrystallographic phase determination that have not been widely used forpeptides were employed: sulfur single-wavelength anomalous diffraction(S-SAD) and post-crystallization incorporation of iodide ions into thecrystal lattice.

S-SAD was used to determine the X-ray crystallographic structure oftrimer 4. The intrinsic anomalous scattering of the sulfur atoms in theasymmetric unit provided sufficient data to determine the X-raycrystallographic phases. Five data sets were collected from a singlecrystal of trimer 4 using an in-house X-ray diffractometer equipped witha rotating copper anode, and the data sets were merged to increase thestrength of the anomalous signal from sulfur. The X-ray crystallographicstructure generated by S-SAD (PDB 5SUS) was used as a search model formolecular replacement to solve the X-ray crystallographic phases of ahigher resolution data set for trimer 4 collected using a synchrotronradiation source (PDB 5SUR).

Iodide ion incorporation and conventional SAD phasing was used todetermine the X-ray crystallographic structure of trimer 3. Toincorporate the iodide ions into the crystal lattice a crystal of trimer3 was soaked in a mixture of crystallization buffer and aqueouspotassium iodide (KI). The X-ray crystallographic structure of theKI-soaked trimer 3 (PDB 5SUU) was used as a search model for molecularreplacement to determine the X-ray crystallographic phases of a higherresolution data set of unsoaked trimer 3 collected using a synchrotronradiation source (PDB 5SUT).

X-Ray Crystallographic Structure and Supramolecular Assembly of Trimer3.

The X-ray crystallographic structure of trimer 3 reveals a symmetrictrimer with three disulfide linkages between the monomeric subunits(FIG. 21). Replacement of L₁₇ and A₂₁ with cysteine was found not toperturb the triangular trimer structure. Trimer 3 is composed of threefolded macrocyclic β-sheets and is virtually identical to the trimersformed by peptides 1 and 2. Trimer 3 maintains the intersheet hydrogenbonds and hydrophobic clustering of amino acid side chains. At eachcorner of trimer 3, the main chain of residue V₁₈ on one monomericsubunit hydrogen bonds with the main chain of residue E₂₂ on theadjacent monomeric subunit (FIG. 22).

The N-methyl groups in trimer 3 are located on the outer hydrogenbonding edges of the trimer. These N-methyl groups block the outerhydrogen-bonding edges of trimer 3 from hydrogen bonding with othertrimers in the crystal lattice. Three ordered water molecules fill thehole in the center of trimer 3, hydrogen bonding with each other andwith the main chain of residue F₂₀.

Clusters of hydrophobic residues in trimer 3 create two surfaces. Thefront surface displays the side chains of residues F₁₉, I₃₂, L₃₄, andV₃₆ as well as the C₁₇-C₂₁ disulfide linkage. This surface is termed the“F₁₉ face”. The back surface displays the side chains of residues V₁₈,F₂₀, and I₃₁. This surface is termed the “F₂₀ face”. Trimer 3 packs onboth the F₁₉ face and the F₂₀ face to form higher-order assemblies inthe crystal lattice.

In the X-ray crystallographic structure of trimer 3, two trimers pack toform a sandwich-like hexamer (FIGS. 23A-23C). In the hexamer, the F₂₀face of one trimer packs against the F₂₀ face of another trimer (FIG.23B). The hexamers further assemble to form columns by stacking on theirF₁₉ faces (FIG. 23C). The columns are arranged in a hexagonal fashion inthe crystal lattice. The hexamer formed by trimer 3 is morphologicallyidentical to the hexamers formed by peptides 1 and 2.

This mode of assembly, in which the hydrophobic faces displayed ontriangular trimers pack together to form hexamers, appears to becharacteristic of triangular trimers formed by amyloid-derivedmacrocyclic β-sheets and β-hairpins. It has also been observed that thismode of assembly occurs with a larger peptide derived from Aβ₁₇₋₃₆; andby a macrocyclic β-sheet peptide derived from β₂-microglobulin.

X-Ray Crystallographic Structure and Supramolecular Assembly of Trimer4.

The X-ray crystallographic structure of trimer 4 reveals a symmetrictrimer that is crosslinked through disulfide linkages between C₁₇ of onemonomeric subunit and C₂₁ of the adjacent monomeric subunit (FIG. 24).Although trimer 4 is composed of three folded macrocyclic β-sheets, itdiffers in conformation from the trimers formed by peptides 1 and 2, andalso differs in conformation from trimer 3. In the three other trimers,the main chains of residues V₁₈ and E₂₂ are hydrogen bonded at thecorners of the trimer. In trimer 4 residues V₁₈ and E₂₂ shift out ofalignment by two residues, such that residue V₁₈ is across from residueF₂₀ and residue E₂₂ is across from ^(δ)Orn (FIG. 25). In furthercontrast to trimer 3, the N-methyl groups in trimer 4 are sequestered inthe center hole of the trimer, exposing the outer hydrogen-bonding edgesand allowing trimer 4 to hydrogen bond with other trimers in the crystallattice.

Clusters of hydrophobic residues in trimer 4 create two surfaces, termedthe “F₁₉ face” and the “F₂₀ face,” respectively. The F₁₉ face displaysthe hydrophobic side chains of residues F₁₉, I₃₂, L₃₄, and V₃₆, as wellas the C₁₇-C₂₁ disulfide linkage. The F₂₀ face displays the hydrophobicside chains of residues V₁₈, F₂₀, and 131.

In the X-ray crystallographic structure of trimer 4, four trimersassemble in a tetrahedral fashion to form a ball-shaped dodecamer (FIG.26). The dodecamer is stabilized by a network of hydrogen bonds amongthe outer edges of the four trimers: the main chains of residues G₃₃ andOrn₃₅ on one trimer hydrogen bond with the main chains of residues I₃₁and ^(δ)Orn on an adjacent trimer. The hydrophobic residues on the F₂₀faces of the four trimers line the inside of the dodecamer, creating alarge hydrophobic cavity approximately 20 nm in diameter.

The ball-shaped dodecamers pack to form a crystal lattice. Within thecrystal lattice, six dodecamers assemble to form annular porelikestructures (FIG. 27A). Hydrophobic packing between the F₁₉ facesdisplayed on the exterior of each dodecamer stabilizes these annularporelike structures. At the interfaces between the dodecamers in theannular pore, two trimers pack to form a sandwich-like hexamer (FIGS.27B and 27C). Each interface is stabilized by hydrophobic packingbetween the side chains of residues on the F₁₉ face and pi stackingbetween the F₁₉ residues on each trimer.

As explained in the preceding paragraphs, trimer 3 and trimer 4 assembleto form different higher-order assemblies within the crystal lattice.Trimer 3 packs to form sandwich-like hexamers, whereas trimer 4assembles to form ball-shaped dodecamers that further assemble to formannular pores. The difference in the position of the N-methyl group onthe two trimers may explain the differences in the assemblies that form.In trimer 4, the N-methyl group on residue F₂₀ is sequestered in thecenter hole of the trimer, exposing the outer hydrogen-bonding edges andallowing trimer 4 to hydrogen bond with the three other trimer 4subunits that comprise the ball-shaped dodecamer. In trimer 3, theN-methyl group on residue G₃₃ prevents dodecamer formation by blockinghydrogen bonds with other trimers. Instead, trimer 3 forms asandwich-like hexamer that is primarily stabilized by packing betweenthe hydrophobic surfaces of the two trimers.

The ball-shaped dodecamers formed by trimer 4 may better represent thetypes of oligomers that full-length Aβ can form. In trimer 4 theN-methyl group is hidden and does not block further assembly. Aβ-hairpin formed by full-length Aβ could assemble in the same fashion toform trimers and dodecamers. This scenario appears likely, sinceβ-hairpins are thought to be the building blocks of some Aβ oligomersand since trimers and dodecamers are known to be important Aβ oligomers(L. Yu, et al., Biochemistry 2009 48, 1870-1877; H. A. Scheidt, et al.,J. Biol. Chem. 2012 287, 22822-22826; T. Doi, et al., Biochem. Biophys.Res. Commun. 2012 428, 458-462; and W. M. Tay, et al., J. Mol. Biol.2013 425, 2494-2508; the disclosures of which are incorporated herein byreference).

Biological Studies and Solution-Phase Biophysical Studies of Trimers 3and 4.

Trimers 3 and 4 constitute the first covalently stabilized oligomersderived from Aβ with well-defined structures and thus provide tools toinvestigate the biological significance of the triangular assembly.Trimers 3 and 4, as well as peptides 1 and 2, were compared in a seriesof biological and biophysical experiments to evaluate the effect ofcovalent stabilization of the trimers, and also to correlate thedifferences in structure and supramolecular assembly observed in theX-ray crystallographic studies with biological and solution-phasebehavior.

Aβ is known to be toxic toward neurons and neuronally derived cells (I.Benilova, et al., 2012, cited supra). To corroborate the toxicity of Aβ,we prepared oligomers of Aβ₄₂ and studied their toxicity toward a humanneuroblastoma cell line, SH-SY5Y. Aβ oligomers were prepared accordingto the procedure developed by Teplow and coworkers using recombinantlyexpressed Aβ₄₂ pretreated with NH₄OH (purchased from rPeptide) (D. B.Teplow, Methods Enzymol. 2006 413, 20-33; and Y. Fezoui, et al.,Amyloid. 2000 7, 166-178; the disclosures of which are incorporatedherein by reference). Under the conditions of the oligomer preparation,Aβ₄₂ forms predominantly monomer, trimer, and tetramer as assessed bySDS-PAGE (FIG. 28A). It was also observed that bands migrated withmolecular weights consistent with a pentamer and hexamer. SH-SY5Y cellswere treated with varying concentrations of Aβ₄₂, and toxicity wasevaluated using a lactate dehydrogenase (LDH) release assay. Aβ₄₂increased LDH release in a dose-dependent manner at concentrations aslow as 2.5 μM, corroborating the toxicity of Aβ₄₂ (FIG. 28B).

It was hypothesized that trimers 3 and 4 may elicit toxicity similarlyto Aβ₄₂. The toxicities of trimers 3 and 4 towards SH-SY5Y cells wereevaluated using an LDH assay, using deionized water (vehicle) andpeptides 1 and 2 as controls. Trimer 4 increased LDH release in adose-dependent manner at concentrations as low as 1.5 μM, indicatingtoxicity toward SH-SY5Y cells (FIG. 29A). LDH release was observed asearly as 48 h after addition to the cells and reached a maximum after 72h. The toxicity of timer 4 does not arise from in situ reduction topeptide 4, as peptides 4 shows little or no toxicity in LDH releaseassays (FIG. 293). Trimer 3 showed far less LDH release than trimer 4.Peptides 1 and 2 showed little or no LDH release.

One of the ways in which A oligomers elicit toxicity is throughinduction of caspase-3 mediated apoptosis. Trimers 3 and 4 wereevaluated for their ability to induce caspase-3 mediated apoptosis usinga rhodamine-based caspase-3 activity assay. At 6 μM, both trimers 3 and4 induced apoptosis within 72 h after addition to the cells, whereaspeptides 1 and 2 show little or no effect (FIG. 30A). Caspase-3 activitylevels after treatment with trimers 3 and 4 is comparable, to that ofthe known caspase-3 activator, staurosporine.

The LDH release and caspase-3 activation studies indicate that trimers 3and 4 behave similarly to oligomers of full-length Aβ, providingevidence for the biological significance of the triangular assembly. Tofurther evaluate how the biological properties of trimers 3 and 4compare to those of full-length Aβ, the reactivity of trimers 3 and 4with the conformation specific antibody A11 was examined. The A11antibody specifically recognizes oligomeric assemblies of Aβ, but doesnot recognize Aβ, monomers or Aβ fibrils. The structures of the Aoligomers recognized by the A11 antibody are not known. We investigatedwhether the A11 antibody recognizes trimers 3 and 4 by dot blotanalysis. Trimers 3 and 4 react with the A11 antibody, but peptides 1and 2 do not (FIG. 30B). These results demonstrate that the A11 antibodyrecognizes trimers 3 and 4, suggesting that oligomers of full-length Aβmay also contain triangular trimers.

The differences in LDH release, caspase-3 activation, and A11 antibodyreactivity between the covalently attached trimers and the peptidessuggest that covalent stabilization of the triangular trimer isnecessary for these small peptides to mimic the oligomers of full-lengthAβ at micromolar concentrations. Furthermore, the difference in LDHrelease between trimer 3 and trimer 4 may reflect differences in thesolution-phase behavior. To understand more about the solution-phasebehavior, size exclusion chromatography (SEC), SDS-PAGE, and circulardichroism (CD) were performed.

SEC studies revealed that trimers 3 and 4 assemble to form higher-orderoligomers in solution. The elution profiles in acetate buffer of trimerswere compared to peptides 1 and 2. Size standards vitamin B12 (1.3 kDa),aprotinin (6.5 kDa), and cytochrome c oxidase (12.4 kDa) eluted at 18.6mL, 15.4 mL, and 13.4 mL, respectively (FIG. 31A). Trimer 3 and 5 elutedat 14.3 mL and at 14.5 mL, respectively. These elution volumes areconsistent with the molecular weight of a hexamer (10.6 kDa). The peaksfor trimers 3 and 4 tail slightly and may reflect a trimer-hexamerequilibrium in which the hexamer predominates. The tail of trimer 4demonstrates a distinct hump at 15.6 mL, suggesting a slow equilibriumbetween the trimer and hexamer.

Under the conditions of the SEC experiments, peptides 1 and 2 do notassemble to form trimers. Peptides 1 and 2 elute at 16.8 mL and 17.3 mL,respectively. These volumes are lower than would be expected for a 1.7kDa monomer and higher than would be expected for a 5.3 kDa trimer,suggesting that peptides 1 and 2 may form dimers in solution.

SDS-PAGE followed by silver staining reveals that trimers 3 and 4assemble to form SDS-stable oligomers (FIG. 31B). Trimer 3 migrates as asingle band at a molecular weight consistent with a hexamer. Trimer 4,in contrast, migrates as two distinct bands: a band consistent with themolecular weight of a dodecamer, and a band consistent with themolecular weight of a trimer. The dodecamer band shows pronouncedstreaking, suggesting equilibrium with lower molecular weight oligomers,such as nonamers and hexamers. Peptides and 2 migrate at molecularweights consistent with either a monomer or dimer.

Circular dichroism spectra reflect the cooperative folding and assemblyof macrocyclic β-sheet peptides. Trimers 3 and 4 exhibit canonical3-sheet character as evidenced by a negative band at ˜217 nm andpositive band at ˜195 nm (FIG. 31C). The spectra of peptides 1 and 2, incontrast, show no well-defined structure. These results indicate thatcovalent stabilization not only locks in conformation, but also promotesfolding of the monomeric subunits into β-hairpins. Table 1 summarizesthe results of the structural and biological studies described above.

TABLE 1 Structures, stoichiometries, and biological activities of trimer4 and trimer 4, and peptides 1 and 2. oligomer size by A11 LDH caspase-3compound PDB ID crystallography SEC SDS-PAGE reactivity releaseactivation trimer 3 5SUT 6 6 6 yes some yes trimer 4 5SUR 6 and 12* 6 3and 12 yes yes yes peptide 1 4NTR 3, 6, and 12 1-2 1-2 no no no peptide2 4NW9 3, 6, and 12 1-2 1-2 no no no *In the X-ray crystallographicstructure of trimer 4, the dodecamers further assemble to form annularporelike structures.Offset Aβ Hairpin Peptides

In the current example, it was set out to explore how altering theresidue pairing of the β-hairpin associated with peptide 1 alters theresulting supramolecular assembly. It was envisioned that a scenario inwhich Aβ₁₅₋₂₃ is free to adopt three pairings with Aβ₀₋₃₆: one in whichAβ₁₇₋₂₃ pairs with Aβ₃₀₋₃₆, one in which Aβ₁₆₋₂₂ pairs with Aβ₃₀₋₃₆, andone in which Aβ_(15_21) pairs with Aβ_(30_36). FIG. 32 illustrates thisconcept. These shifts in pairing sequentially pull Lys₁₆ and Gln₁₅ intothe upper β-strand while pushing Asp₂₃ and Glu₂₂ out of the β-strand andinto the loop.

Macrocyclic β-hairpin peptides 5, 6, and 7 were designed to explore theconcept embodied in FIG. 32A and characterized the resulting assembliesby X-ray crystallography. The native Met₃₅ was incorporated into each ofthese peptides, rather than the α-linked ornithine isostere, to bettermimic the native β-hairpins. Phe₁₉ was replaced withpara-iodophenylalanine (Phe^(I)) to facilitate crystallographic phasedetermination by single wavelength anomalous diffraction phasing (R. K.Spencer and J. S. Nowick, Israel J. Chem. 2015, 55, 689-710, thedisclosure of which is incorporated herein by reference). Peptides 5 to7 were synthesized and crystalized, and their crystallographicstructures were determined using procedures that we have previouslyreported (FIG. 32B; Seq. ID Nos. 26-31). It is noted, however, thatsonication permits the dissolution of Met₃₅-containing peptides, whichis substantially less soluble then Orn₃₅-containing peptide 1.

Peptide 5 assembles in an identical fashion to peptide 1, formingtriangular trimers that further assemble into spherical dodecamers (FIG.33A-F). In each trimer, three monomers occupy the edges of anequilateral triangle (FIG. 33A). The Aβ₁₇₋₂₃ β-strands of the monomerscome together, hydrogen bonding to each other and to three watermolecules that sit in the center of each trimer. The Aβ₃₀₋₃₆ β-strandsof the monomers form the outer edges of the trimer. The side chains ofLeu₁₇, Phe^(I) ₁₉, and Val₃₆ of one monomer pack against the side chainsof Ala₂₁, Asp₂₃, Ile₃₂, and Leu₃₄ from an adjacent monomer at the threevertices of the trimer. Four trimers further assemble in a tetrahedralarrangement into a loosely packed hollow dodecamer (FIG. 33B). Theasymmetric unit of the crystal lattice formed by peptide 5 contains 16peptide molecules, which assemble into four crystallographically uniquedodecamers, each containing four unique peptide molecules. The fourdodecamers, however, are very similar in structure. The diameter of thedodecamer spans 4-6 nm, depending on the points of measure, while itscentral cavity spans ca. 1.4 nm. The side chains of Phe^(I) ₁₉, Leu₃₄,and Val₃₆ line the cavity. The dodecamers further pack to form thelattice, with each interface between two dodecamers constituting asandwich-like hexamer (FIG. 33C). The side chains of Phe₂₀, Glu₂₂, andIle₃₁ pack against one another in the interior of the hexamer.

Peptide 6 assembles into compact ball-shaped dodecamers that differ fromthose formed by peptide 5 (FIG. 33D). The dodecamer formed by peptide 5comprises discrete triangular trimers, while the dodecamer formed bypeptide 6 comprises fused triangular trimers. Each trimer in thedodecamer formed by peptide 6 shares three edges with the three adjacenttrimers. As a result, the trimers are not discrete entities within theball-shaped dodecamer, but instead are fused like the benzene rings ofnaphthalene or graphite.

Two types of trimers make up the ball-shaped dodecamer formed by peptide6 (FIGS. 33E and 33F). The two types of trimers differ in the placementof the Aβ₁₆₋₂₂ and Aβ₃₀₋₃₆ β-strands. The Aβ₁₆₋₂₂ β-strands of themonomers hydrogen bond to each other within the trimer depicted in FIG.33E, while the Aβ₃₀₋₃₆ β-strands hydrogen bond to each other within thetrimer depicted in FIG. 33F. The outer edges of the trimer depicted inFIG. 33E lie within three different trimers, like the one depicted inFIG. 33F. Conversely, the outer edges of the trimer depicted in FIG. 33Flie within three different trimers, like the one depicted in FIG. 33E.Three water molecules occupy the center of the trimer depicted in FIG.33E. The three N-methyl groups occupy the center of the trimer depictedin FIG. 33F, in lieu of three water molecules.

The ball-shaped dodecamer formed by peptide 6 is hollow, like thedodecamer formed by peptide 5. The diameter of the ball-shaped dodecamerspans 3-4 nm depending on the points of measure, while its centralcavity spans ca. 1.0 nm. The side chains of Phe^(I) ₁₉ line the cavity,while the exterior surface of the dodecamer displays the side chains ofLys₁₆, Val₁₈, Phe₂₀, Glu₂₂, Alan, Ile₃₂, Leu₃₄, and Val₃₆. Unlike thedodecamers formed by peptide 5, the dodecamers formed by peptide 6 donot form sandwich-like hexamers. Instead these dodecamers packhexagonally and stack like cannonballs.

The dodecamers formed by peptides 5 and 6 share similar themes inself-assembly, as both are composed of triangular trimer subunits.Mapping the triangular subunits of each dodecamer onto an octahedronhighlights these similarities, as well as key differences (FIG. 34). Inthe dodecamer formed by peptide 5, the four trimers occupy four of theeight triangular faces of the octahedron. The interfaces between thetrimers define the remaining four triangular faces. In the dodecamerformed by peptide 6, each monomer occupies one edge of the octahedron,and each trimer defines one of the eight triangular faces of theoctahedron. At each of the six vertices of the octahedron, four monomersof peptide 6 form an eight-stranded β-barrel-like opening. An analogousopening is absent in the dodecamer formed by peptide 5. Thehydrogen-bonding network that helps stabilize both dodecamers is moreextensive in the dodecamer formed by peptide 6, which contains 36additional intermolecular hydrogen bonds beyond those that compose thehydrogen-bonding network in the dodecamer formed by peptide 5. Thedodecamer formed by peptide 6 is more densely packed than the dodecamerformed by peptide 5. Assembly of peptide 6 into a dodecamer buries ca.10,800 Å² of surface area, whereas assembly of peptide 5 into adodecamer buries only ca. 8,100 Å². It is not obvious from theirsequences or structures why peptide 6 forms a more compact dodecamerthat differs from that of peptide 5.

In contrast to the discrete oligomers formed by peptides 5 and 6,peptide 7 forms a fibril-like assembly (FIG. 35). Each monomer ofpeptide 7 hydrogen bonds with the two neighboring monomers along thefibril axis. The interface between monomers constitutes a parallelβ-sheet with three intermolecular hydrogen bonds in which Leu₁₇, Val₁₈,and Phe^(I) ₁₉ pair with □Orn₂, Alan, and Ile₃₁. The N-methyl group onGly₃₃ blocks formation of a fully hydrogen-bonded interface, pryingapart the β-sheets and requiring a water molecule to bridge a hydrogenbond between the NH group of Phe₂₀ and the carbonyl group of Ile₃₁. Eachmonomer is flipped upside down with respect to the neighboring monomersin the fibril such that the surfaces of the monomers are displayed in analternating pattern along the surface of the fibril: one monomerdisplays its top surface, the next monomer displays its bottom surface,and so on down the fibril (FIG. 36).

The fibril-like assemblies formed by peptide 7 are not flat; insteadthey zig-zag in the x-z plane as depicted in FIG. 35. The fibrils stackalong the x-axis, creating densely packed layers in the x-z plane. Thelayers run in opposite directions to one another. Within each layer, allof the N-methyl groups point in the same direction. In the green layersin FIG. 35, the N-methyl groups point in the negative z direction, whilein the cyan layers, the N-methyl groups point in the positive zdirection (FIG. 36). The lay layers pack tightly through hydrophobicinteractions, with the top surface of a monomer in one layer packingagainst the bottom surface of its neighbor in the adjacent layer. Thisheterofacial packing of residues contrasts the exclusively homofacialpacking of residues in the dodecamers formed by peptides 5 and 6. It isnot obvious why peptide 7 forms fibril-like assemblies in the crystallattice, instead of the trimers and dodecamers formed by peptides 5 and6.

The different assemblies of peptides 5-7 reflect the rich and diversemodes of β-hairpin self-assembly and illustrate their propensity to formboth fibril-like and oligomeric assemblies. The assembly of β-hairpinsinto dodecamers comprising triangular trimer subunits offers an alluringhigh-resolution model for the enigmatic oligomers reported forfull-length Aβ. Townsend et al. reported that Aβ trimers inhibitlong-term potentiation (M. Townsend, et al., J. Physiol. 2006, 572,477-492, the disclosure of which is incorporated herein by reference).Lesne et al. reported that putative dodecamers of Aβ, termed Aβ*56,cause memory deficits in a mouse model of Alzheimer's disease (S. Lesne,et al., Nature 2006, 440, 352-357, the disclosure of which isincorporated herein by reference). The putative Aβ*56 dodecamers appearto be composed of trimer subunits. The trimers and dodecamers formed bypeptides 5 and 6 provide two models of how Aβ may oligomerize inAlzheimer's disease. The formation of trimeric oligomers is also acommon theme of full-length peptides and proteins associated with otheramyloid diseases (B. Winner, et al, Proc. Natl. Acad. Sci. U.S.A. 2011,108, 4194-4199, the disclosure of which is incorporated herein byreference).

Offsetting the residue pairings of the two β-strands within a β-hairpinmay dramatically alter the self-assembly. The approach of systematicallyvarying the residue pairings in constrained macrocyclic β-hairpins hasrevealed a compact ball-shaped dodecamer containing fused trimers andstabilized by an extensive network of hydrogen bonds. The importance ofresidues 15-36 in the aggregation of full-length Aβ makes peptides 5-7relevant models for the assembly of full-length Aβ. It is possible thatfull-length Aβ may be able to fold and assemble in a similar fashion.The relationship between the sequence of a β-hairpin and its mode ofassembly is still unknown.

Further Characterization of Peptide Oligomerization

In the examples in the preceding sections, X-ray crystallographicstructures of oligomers formed by macrocyclic β-sheet peptides designedto mimic β-hairpins from amyloidogenic peptides and proteins weredescribed. In some of these examples, β-hairpin peptides contain twoheptapeptide β-strand fragments locked in an antiparallel β-sheet by twoδ-linked ornithine (^(δ)Orn) turn mimics, and also contain an N-methylgroup that blocks uncontrolled aggregation. These design features permitcrystallization of the β-hairpin peptides and structural elucidation ofthe higher-order oligomers they can form. The β-hairpin peptides havetwo surfaces: a major surface that displays eight of the fourteen sidechains, and a minor surface that displays the remaining six side chains.FIG. 37 shows a generic structure of these β-hairpin peptides andhighlights the major and minor surfaces in red and blue.

The elucidated the X-ray crystallographic structures of oligomers formedby β-hairpin peptides derived from Aβ revealed the propensity forβ-hairpin peptides to form oligomers in the crystal state, includingdimers, trimers, hexamers, octamers, nonamers, and dodecamers. Thedifferent oligomers identified in these examples demonstrate thediversity and polymorphism of the structures that differentamyloid-derived β-hairpin peptides can form.

The X-ray crystallographic structures of oligomers formed by β-hairpinpeptide 2, which is derived from an Aβ₁₇₋₃₆ β-hairpin (FIG. 38; Seq. IDNos. 20, 21, and 32). Peptide 2 contains Aβ₁₇₋₂₃ and Aβ₃₀₋₃₆ β-strandslinked by two ^(δ)Orn turn units; the ^(δ)Orn turn that links Asp₂₃ andAlan replaces the Aβ₂₄₋₂₉ loop of the Aβ₁₇₋₃₆ β-hairpin. Peptide 2 alsocontains an N-methyl group on Phe₂₀ and α-linked ornithine at position35 as a hydrophilic isostere of methionine. The X-ray crystallographicstructure reveals that peptide 2 assembles hierarchically to form atriangular trimer that further assembles with a second triangular trimerto form a sandwich-like hexamer (FIG. 39).

In the example, it was set out to explore how shifting registration byone amino acid toward the N-terminus affects the structural andbiological properties of a β-hairpin peptide. Offsetting β-hairpinregistration is significant, because it changes both the pairings of theresidues within the β-hairpin and the surfaces upon which the sidechains are displayed. In the Aβ₁₇₋₃₆ β-hairpin, from which peptide 2 isderived, Ile₃₁ pairs with Glu₂₂; in the shifted Aβ₁₆₋₃₆ β-hairpin, Ile₃₁pairs with Ala₂₁. In the Aβ₁₇₋₃₆ β-hairpin, the side chain of Glu₂₂shares the same surface as the side chain of Ile₃₁; in the Aβ₁₆₋₃₆β-hairpin, the side chain of Glu₂₂ is on the opposite surface. We findthat the resulting shifted β-hairpin peptide not only assembles in thecrystal state to form oligomers, but also exhibits both solution-phaseassembly and toxicity reminiscent of amyloid oligomers.

The X-ray crystallographic, solution-phase, and biological studies ofpeptide 8, which is designed to mimic the A₁₁₆₋₃₆ β-hairpin (FIG. 40;Seq. ID Nos. 33-35), is described. Peptide 8 contains Aβ₁₆₋₂₂ andAβ₃₀₋₃₆ β-strands linked by two ^(δ)Orn turn units, an N-methyl group onPhe₁₉, and the native methionine residue at position 35. Peptide 8 runsas a hexamer in SDS-PAGE and appears to form dimers and trimers in sizeexclusion chromatography (SEC). The oligomers formed by peptide 8 aretoxic toward the human neuroblastoma cell line SH-SY5Y. X-raycrystallography reveals that peptide 8 also assembles to form a hexamerin the crystal state. The hexamer may be thought of as being composed ofeither dimers or trimers. The hexamer formed by peptide 2 is significantbecause it shares key characteristics with the oligomers formed byfull-length amyloidogenic peptides and proteins and provides astructural model for an oligomer of Aβ.

Oligomerization of Peptide 8

Peptide 8 assembles to form a hexamer in SDS-PAGE. Tricine SDS-PAGEfollowed by silver staining shows that the 1.8 kDa peptide 8 migratesjust above the 10 kDa band of the ladder (FIG. 41A). The band frompeptide 8 is comet-shaped and streaks downward, suggesting that thehexamer is in equilibrium with lower molecular weight species. Tofurther confirm the oligomerization state of peptide 1, it was comparedto covalent trimers 3 and 4 (FIGS. 19A and 19B), which was previouslydetermined to migrate respectively as 10.6 kDa hexamers and 21.2 kDadodecamers in equilibrium with the 5.3 kDa trimers. Peptide 8 migratesat the same molecular weight as the hexamer band of trimer 3, providingfurther evidence that peptide 8 assembles to form a hexamer in SDS-PAGE.In contrast, peptide 2 does not assemble to form a hexamer in SDS-PAGE.Peptide 2 migrates well below the trimer band of trimer 4, and slightlybelow the 4.6 kDa band of the ladder, suggesting that peptide 2 migratesas a monomer or dimer.

Size exclusion chromatography reveals that peptide 8 also assembles toform oligomers in the absence of SDS. The elution profile of peptide 8was compared to the size standards vitamin B12, aprotinin, andcytochrome c, as well as peptide 2. Peptide 8 elutes as a broad peakwith three distinct humps (FIG. 41B). The elution volumes of the humpsare consistent with the molecular weights of a monomer, dimer, andtrimer, respectively. The broadness of the humps suggests moderatelyslow exchange between the trimer, dimer, and monomer. Peptide 2 elutesas two distinct peaks: a larger peak with an elution volume consistentwith the molecular weight of a dimer, and a smaller peak with an elutionvolume consistent with the molecular weight of a trimer (FIG. 41B).Table 2 summarizes the SEC data for peptides 2 and 8.

TABLE 2 Size exclusion chromatography data for peptides 2, 8, 9 and 10.molecular elution compound weight volume (mL) oligomer size peptide 21.74 kDa 16.2, 15.1 dimer, trimer peptide 8 1.77 kDa 17.0, 16.1, 14.8monomer, dimer, trimer peptide 9 1.79 kDa 17.6 monomer peptide 10 1.72kDa 17.0 monomer vitamin B12 1.3 kDa 17.8 aprotinin 6.5 kDa 14.6cytochrome c 12.4 kDa 12.4

These solution-phase studies show that peptide 8 assembles to formoligomers in solution. In SDS-PAGE, peptide 8 assembles to form ahexamer. In SEC in Tris buffer, peptide 8 assembles to form dimers andtrimers. These results suggest the intriguing hypothesis that thehexamer in SDS-PAGE may be composed of dimers or trimers that furtherassemble to form a hexamer in the lipophilic environment of SDSmicelles. X-ray crystallography was performed to gain insights into thestructures of these oligomers, and thus further explore this hypothesis.

X-Ray Crystallographic Structure of Peptide 8

Peptide 8 afforded crystals suitable for X-ray diffraction from aqueousHEPES buffer with sodium citrate and isopropanol. To determine the X-raycrystallographic phases of peptide 8, a crystal of the peptide wassoaked in potassium iodide to incorporate iodide ions into the crystallattice and performed conventional single-wavelength anomalousdiffraction (SAD) phasing (A. G. Kruetzer, et al., Am. Chem. Soc. 2016138, 4634-4642; Z. Dauter, M Dauter, and K. R. Rajaashankar Acta.Crystallogr. D Biol. Crystallogr. 2000 56, 232-237; and R. K. Spencerand J. S. Nowick 2015, cited supra; the disclosures of which areincorporated herein by reference). The X-ray crystallographic structureof the KI-soaked peptide 8 (PDB 5W4I) was then used as a search modelfor molecular replacement to determine the X-ray crystallographic phasesof a higher resolution data set of unsoaked peptide 8, which wascollected using a synchrotron radiation source (PDB 5W4H).

The X-ray crystallographic structure of peptide 8 reveals that thepeptide folds to form a twisted β-hairpin. The side chains displayed onthe major and minor surfaces of peptide 8 differ from those displayed onthe major and minor surfaces of peptide 2. The major surface of thepeptide 8 β-hairpin displays the side chains of Lys₁₆, Val₁₈, Phe₂₀,Glu₂₂, Alan, Ile₃₂, Leu₃₄, and Val₃₆, while the major surface of thepeptide 2 β-hairpin displays the side chains of Leu₁₇, Phe₁₉, Ala₂₁,Asp₂₃, Alan, Ile₃₂, Leu₃₄, and Val₃₆ (FIG. 42). The minor surface of thepeptide 8 β-hairpin displays the side chains of Leu₁₇, Phe₁₉, Ala₂₁,Ile₃₁, Gly₃₃, and Met₃₅, while the minor surface of the peptide 2β-hairpin displays the side chains of Val₁₈, Phe₂₀, Glu₂₂, Ile₃₁, Gly₃₃,and Orn₃₅ (FIG. 42). Thus, the minor surface of peptide 8 is whollyhydrophobic, while the minor surface of peptide 2 is not.

In the X-ray crystallographic structure of peptide 8, six β-hairpinmonomers assemble to form a hexamer. The hexamer is composed of smalleroligomers and can be interpreted either as a trimer of dimers or as adimer of trimers. FIG. 43 shows the structure of the hexamer andillustrates these two interpretations. In FIG. 43, one dimer subunit iscolored green and one trimer subunit is colored cyan. The followingsubsections detail the structure of the hexamer as well as thestructures of the component dimers or trimers.

Hexamer.

The hexamer formed by peptide 8 resembles a barrel with three openings(FIG. 44). The interior of the barrel is filled with the side chains ofresidues on the minor surface of peptide 8—Leu₁₇, Phe₁₉, Ala₂₁, Ile₃₁,Gly₃₃, and Met₃₅—creating a packed hydrophobic core that stabilizes thehexamer (FIG. 44). A network of hydrogen bonds between the main chainsof the monomer subunits further stabilizes the hexamer. The outersurface of the hexamer displays the side chains of residues on the majorsurface of peptide 8—Lys₁₆, Val₁₈, Phe₂₀, Glu₂₂, Ala₃₀, Ile₃₂, Leu₃₄,and Val₃₆.

The hexamer formed by peptide 8 is more hydrogen bonded and betterpacked than the hexamer formed by peptide 2 (FIG. 45). The hexamerformed by peptide 8 forms a continuous hydrogen-bonding networkcontaining 30 intermolecular hydrogen bonds, whereas the hexamer formedby peptide 2 does not form a continuous hydrogen-bonding network andcontains only 18 intermolecular hydrogen bonds. In the hexamer formed bypeptide 2, each β-hairpin monomer is only hydrogen bonded to the twoadjacent β-hairpin monomers within the triangular trimer; in the hexamerformed by peptide 8, each β-hairpin monomer is hydrogen bonded not onlyto the two adjacent monomers within the triangular trimer, but also tothe adjacent monomer within the β-sheet dimer. For these reasons, thehexamer formed by peptide 8 can either be interpreted as a trimer ofβ-sheet dimers or as a dimer of triangular trimers, whereas the hexamerformed by peptide 2 is unambiguously a dimer of triangular trimers.

Six sets of side chains from Leu₁₇, Phe₁₉, Ala₂₁, Ile₃₁, and Met₃₅ packtogether to form a hydrophobic core that stabilizes the hexamer formedby peptide 8. While the minor surface of peptide 8 displays fivehydrophobic side chains, which of peptide 2 displays only three—Val₁₈,Phe₂₀, and Ile₃₁. The hexamer formed by peptide 2 lacks the massivehydrophobic core and is only loosely packed at the interface betweentrimers. The buried surface area of the hexamer formed by peptide 8 is5102 Å², whereas the buried surface area of the hexamer formed bypeptide 2 is only 3514 Å².

Dimer.

Two peptide 8 β-hairpin monomers assemble edge-to-edge to form ahydrogen-bonded dimer, creating a four-stranded antiparallel β-sheet(FIG. 46A). Three such dimers make up the hexamer. The β-hairpinmonomers are shifted out of registration by two residues toward theN-termini, such that Alan on one monomer is across from Leu₃₄ on theadjacent monomer (FIG. 46B). Four intermolecular hydrogen bonds betweenIle₃₁ and Gly₃₃ of one monomer and Gly₃₃ and Ile₃₁ of the adjacentmonomer help stabilize the dimer.

The β-sheet dimer has two surfaces: one surface displays the side chainsof residues on the major surface of peptide 8; the other surfacedisplays the side chains of residues on the minor surface of peptide 8(FIG. 47). Hydrophobic packing between the side chains of residues onthe minor surface further stabilizes the dimer: Leu₁₇, Phe₁₉, and Ile₃₁on one monomer pack against Ile₃₁, Phe₁₉, and Leu₁₇ on the adjacentmonomer. There are no substantial intermolecular contacts between theside chains of residues on the major surface of the dimer.

Trimer.

Three peptide 8 β-hairpin monomers assemble to form a triangular trimer(FIG. 48A). Two such trimers make up the hexamer. The trimer isstabilized by intermolecular edge-to-edge hydrogen bonds betweenmonomers, which create four-stranded β-sheets at each corner of thetrimer. At each corner, the main chain of ^(δ)Orn of one monomerhydrogen bonds with the main chain of Ala₂₁ of the adjacent monomer, andthe carbonyl of Phe₁₉9 of one monomer hydrogen bonds with the NH ofLeu₁₇ of the adjacent monomer (FIG. 48B).

The triangular trimer has two surfaces that display the amino acid sidechains of the major surfaces and the minor surfaces of the componentβ-hairpin monomers (FIG. 49). Hydrophobic packing between the sidechains of residues on the minor surface further stabilizes the trimer:Met₃₅, Leu₁₇, and Phe₁₉9 on one monomer pack against Ala₂₁, Ile₃₁, andPhe₁₉9 on the adjacent monomer. There are no substantial intermolecularcontacts between side chains of residues on the major surface of thetrimer.

The hexamer, trimer, and dimer observed in the X-ray crystallographicstructure of peptide 8 recapitulate the oligomers observed in SDS-PAGEand SEC. The assembly of the hexamer from either dimers or trimers mayexplain how the peptide 8 dimers and trimers observed in SEC cometogether to form the hexamer in SDS-PAGE. The structure of the hexamershows key stabilizing contacts, such as edge-to-edge hydrogen bondingand hydrophobic packing. To better understand the importance of thesecontacts in the solution-phase oligomerization of peptide 8, peptides 9and 10 were designed. The following sections describe studies of thesepeptides and also provide insights into why Aβ₁₆₋₃₆-derived peptide 8forms a hexamer in SDS-PAGE, but Aβ₁₇₋₃₆-derived peptide 2 does not.

N-Methylation of Peptide 8 Disrupts Oligomerization

To test whether the hexamer observed in SDS-PAGE is similar in structureto the hexamer observed crystallographically, a homologue containing anadditional N-methyl group designed to disrupt hexamer formation wasprepared. Peptide 9 is a homologue of peptide 8 bearing an additionalN-methyl group on Gly₃₃ (FIG. 5A; Seq. ID Nos. 36 and 37). In the X-raycrystallographic structure of the hexamer formed by peptide 8, thebackbone of Gly₃₃ on one monomer hydrogen bonds with the backbone ofIle₃₁ on an adjacent monomer (FIG. 46B). Introduction of an N-methylgroup on Gly₃₃ should prevent hydrogen bonding and thus disrupt thehexamer. In SDS-PAGE, peptide 9 does not migrate as a hexamer (FIG.41A). Instead, peptide 9 migrates similarly to peptide 2, and thusappears to run as a monomer or dimer. This result supports a model inwhich the hexamer formed by peptide 8 in SDS-PAGE is similar instructure to the hexamer observed crystallographically. In SEC, peptide9 elutes at a volume consistent with the molecular weight of a monomer(Table 2), further demonstrating that N-methylation on Gly₃₃ disruptsoligomer formation.

Mutation of Peptide 2 Induces Oligomerization

The SDS-PAGE and X-ray crystallographic studies of peptides 2 and 9demonstrate that shifting the registration of a β-hairpin peptideaffects its oligomerization. In the X-ray crystallographic structures,the hexamer formed by peptide 8 is better packed and has more hydrogenbonds than the hexamer formed by peptide 2. In SDS-PAGE, peptide 8assembles to form a hexamer, whereas peptide 2 does not. The differencein the hydrophobicity and charge of the minor surfaces of peptides 2 and9 may explain this difference in oligomerization. The minor surface ofpeptide 2 displays two charged hydrophilic side chains and threehydrophobic side chains, whereas the minor surface of peptide 8 displaysfive hydrophobic side chains (FIG. 51).

To explore the importance of charge and hydrophobicity inoligomerization, peptide 10 was prepared (FIG. 50B). Peptide 10 is atriple mutant of peptide 2, with L₁₇K, E₂₂A, and Orn₃₅M mutations.Peptide 10 may be thought of as a chimera in which three residues ofpeptide 8 are grafted onto peptide 2 to eliminate charge on the minorsurface. In peptide 10, Ala₂₂ and Met₃₅ occupy the same sites on theminor surface as Ala₂₁ and Met₃₅ in peptide 8. The Lys₁₇ residue inpeptide 10 sits on the major surface, occupying the same site as Lys₁₆in peptide 8 and providing charge to enhance solubility. The remaining11 residues of peptide 10 are identical to those of peptide 2.

SDS-PAGE reveals that peptide 10 assembles to form an oligomer thatmigrates at a slightly higher molecular weight than the hexamer formedby peptide 8 (FIG. 41A). Replacement of the charged residues withhydrophobic residues on the minor surface of peptide 2 converts apeptide that does not form oligomers in aqueous SDS to a peptide thatoligomerizes. This experiment confirms the importance of an uncharged,hydrophobic surface in the oligomerization of β-hairpin peptides. InSEC, peptide 10 elutes at a volume consistent with the molecular weightof a monomer (Table 2), suggesting that SDS promotes oligomerization ofpeptide 10 in the SDS-PAGE experiment.

The slightly higher position of the peptide 10 oligomer band in SDS-PAGEsuggests that the oligomer formed by peptide 10 may differ in structurefrom the hexamer formed by peptide 8. To gain insights into thestructure of the oligomer formed by peptide 10, X-ray crystallographywas performed. Peptide 10 afforded crystals suitable for X-raydiffraction in aqueous HEPES buffer with potassium chloride andpentaerythritol propoxylate. The X-ray crystallographic phases ofpeptide 10 was determined by sulfur single-wavelength anomalousdiffraction (S-SAD) using the anomalous signal from the sulfur inmethionine (Q. Liu, et al., Science 2012 336, 1033-1037; and G. N.Sarma, et al., Acta. Crystallogr. D Biol. Crystallogr. 2006 62, 707-716;the disclosures of which are incorporated herein by reference).

X-ray crystallography reveals that peptide 10 folds to form β-hairpinssimilar to those formed by peptides 2 and 9 (FIG. 51). The minor surfaceof peptide 10 is nearly identical to that of peptide 8, except thatVal₁₈ takes the place of Leu₁₇. Peptide 10 assembles differently thanpeptides 2 and 9, forming packed columns in the crystal lattice ratherthan discrete oligomers (FIG. 52B). The columns are composed ofantiparallel β-sheet dimers that are laminated on both faces throughhydrophobic interactions. Each dimer consists of an antiparallel β-sheetformed by two peptide 10 β-hairpins (FIG. 52A). The dimer is shifted outof registration by two residues toward the C-termini, such that Met₃₅pairs with Gly₃₃. The oligomer formed by peptide 10 in SDS-PAGE might becomposed of three or four of these dimers packing through hydrophobicinteractions.

Biological Studies of Peptides 2, 8, 9 and 10

Many oligomers formed by full-length Aβ are toxic toward cells (I.Benilove, E. Karan, and B. De Strooper, Nat. Neurosci. 2012 15, 349-357;and M. E. Larson and S. E. Lesne J. Neurochem. 2012 120, 125-139; thedisclosures of which are incorporated herein by reference). To testwhether the oligomers formed by peptide 8 are also toxic, the toxicityof peptide 8 toward neuronally derived SH-SY5Y cells were evaluatedusing a lactate dehydrogenase (LDH) release assay. Peptide 8 and 10 werecompared to investigate how the hexamer-forming Aβ₁₆₋₃₆-derived peptidecompares to a non-oligomerizing homologue. The toxicity of peptides 2and 11 were also evaluated to better understand the relationship betweenoligomerization and toxicity.

Peptide 8 shows an increase in LDH release at concentrations as low as50 μM, indicating toxicity toward SH-SY5Y cells (FIG. 53). Peptide 9,the non-oligomerizing homologue of peptide 8, is not toxic towardSH-SH5Y cells at concentrations as high as 200 μM, suggesting thatoligomerization of peptide 8 to form a hexamer is important fortoxicity. No dose dependence is observed in the LDH release induced bypeptide 8 at concentrations of 50,100, and 200 μM, suggesting thatoligomerization is cooperative and toxicity occurs above a criticalconcentration. Peptide 2 is toxic toward SH-SY5Y cells at concentrationsas low as 100 μM, and peptide 10 is toxic toward SH-SY5Y cells atconcentrations as low as 50 μM.

The onset of toxicity of peptides 2, 8, and 10 between 25 μM and 100 μMreflects the propensity of the hydrophobic peptides to form oligomers inthe presence of the lipophilic cell membranes. In this model, none ofthe peptides are oligomeric in cell membranes at 25 μM. As theconcentration is increased, oligomerization occurs, the oligomersdisrupt the integrity of the cell membranes, and cell damage or deathoccurs.

Crystallographically Based Model of an Aβ₁₂₋₄₀ Hexamer

It is hypothesized that the full-length Aβ peptide can assemble in thesame fashion as peptide 8 to form a barrel-like hexamer composed ofβ-sheet dimers or triangular trimers. To better understand what ahexamer containing the Aβ₂₃₋₂₉ loop and additional N- and C-terminalresidues might look like, Aβ₁₂₋₄₀ was modeled into the crystallographiccoordinates of the hexamer. Residues 23-29 (DVGSNKG), 12-15 (VHHQ), and37-40 (GGW) were built into the crystallographic coordinates of the sixpeptide 8 monomers that comprise the hexamer, and replica-exchangemolecular dynamics (REMD) was performed to generate realisticconformations of the loops and the N- and C-terminal regions of theβ-hairpins (FIG. 54) (Y. Sugita and Y Okamoto, Chem. Phys. Lett. 1999314, 141-151; and J. C. Phillips, et al., J. Comput. Chem. 2005 26,1781-1802; the disclosures of which are incorporated herein byreference).

The REMD simulation shows that full-length Aβ could form a barrel-likehexamer. The hexamer can accommodate the Aβ₂₃₋₂₉ loop and the remainingN- and C-terminal residues without steric clashes. In a hexamer formedby full-length Aβ, the loops from two monomers and the N- and C-terminifrom another two monomers would extend past the barrel-like openings.The loops might fold over the barrel-like openings and shield thehydrophobic core of the hexamer, which would otherwise be exposed tosolvent.

Antibody Generation and Characterization

In this example, antibodies are generated that have high affinity foroligomeric species of Aβ but not monomers or fibrils. Furthermore, thegenerated antibodies are highly reactive in brain tissue of AD patientsand transgenic AD mice, but not of healthy brain tissue. These datasuggest that these generated antibodies are specific for solubleoligomers of Aβ, but do not react with Aβ monomers or insoluble fibrils.

Polyclonal antibodies were generated using trimer 4 (FIG. 19B; Seq. IDNos, 24 and 25) chemically conjugated to the carrier protein hemocyanin.Conjugation of was performed using standard EDC coupling chemistry, asunderstood in the art. Next, the trimer 4-hemocyanin conjugate was usedto immunize rabbits in either complete Freund's adjuvant or incompleteFreund's adjuvant. After about 30 days, ˜50 ml of blood was drawn fromthe immunized rabbit, and either plasma or serum, containing thepolyclonal antibodies, was prepared for further purification. Thepolyclonal antibodies were purified from the plasma or serum viaspecific affinity chromatography using timer 4 as a ligand. Antibodieswere then separated from the ligand and subsequently resuspended inappropriate storage buffer. The purified antibodies were subsequentlycharacterized for their affinity and specificity.

Shown in FIG. 55 is a dot plot of the trimer affinity-purifiedantibodies bound to various concentrations of peptides and trimers. Theaffinity-purified antibodies do not appreciably appear to bind topeptides 1 and 3, even at concentrations of 1.0 mg/mL. Theaffinity-purified antibodies, however, has a strong affinity for trimers3 and 4, as can be seen in at 0.25 and 0.06 mg/mL concentrationsrespectively.

The trimer affinity-purified antibodies were also tested in anenzyme-linked immunosorbant assay (ELISA) (FIG. 56). In this assay,peptides 1 and 2 and trimers 3 and 4 were fixed to a 96-well plate at afixed concentration. Affinity-purified antibodies, conjugated with afluorophore, were incubated with the fixed peptides and trimers, andthen washed to remove excess antibodies. Absorbance of the fluorophoreis shown in FIG. 56. As shown in the chart, the affinity-purifiedantibodies have very high affinity for both trimers, but not thepeptides, at 2.6 and 12.8 ng/mL of antibody. These results confirm thatthe trimer affinity-purified antibodies are specific for trimeric Aβoligomers, but not the monomeric peptides.

The trimer affinity-purified antibodies were compared to a popular Aβantibody known as the “6E10” antibody, which is available from manycommercial retailers. The antibody is monoclonal and specificallyrecognizes the first sixteen amino acids of Aβ (i.e., Aβ₁₋₁₆). FIG. 57displays compares the ability of the affinity-purified antibodies andthe 6E10 antibody to recognize recombinant Aβ₁₋₄₀ and Aβ₁₋₄₂. In thisexperiment, cell extracts were created from human cultured cells thatexpressed Aβ₁₋₄₀ and Aβ₁₋₄₂. The cell lysates were prepared and run inan SDS-PAGE gel using an electrophoresis apparatus, and then transferredonto a membrane for Western blot analysis. As shown in FIG. 57, the 6E10antibody has a high affinity for the monomers, dimers, and tetramers ofAβ₁₋₄₀ and Aβ₁₋₄₂. Furthermore, the 6E10 antibody does not clearlyidentify the soluble trimers, hexamers, nonamers, and dodecamers. Theaffinity-purified antibodies, on the other hand, clearly identify anddistinguish the soluble trimers, hexamers, nonamers, and dodecamerswithout any signal for the monomers, dimers, or tetramers. These resultsclearly show that the trimer affinity-purified antibodies outperformcommercially available antibodies on affinity and specificity of solubletrimer and higher order oligomers.

The trimer affinity-purified antibodies were also tested using humanbrain extracts and fixed tissue slices. In these experiments, extractsand tissue slices of an AD patients and healthy control were preparedaccording to standard protocols known in the art. The extracts were runin an SDS-PAGE gel using an electrophoresis apparatus. The extracts weretransferred to a membrane for Western blot analysis, depicted in FIG.58. As the figure shows, the antibodies recognized soluble Aβ trimersand hexamers in an extracellular fraction. The antibodies alsorecognized trimers, hexamers and dodecamers in the membrane-enrichedfraction. As expected, the AD patient exhibited a higher level ofsoluble Aβ oligomers than the healthy control.

FIG. 59 depicts fluorescent images of human brain tissue slices takenfrom the superior temporal gyrus. The trimer affinity-purifiedantibodies (in yellow) displayed discreet, specific staining in theextranuclear and extracellular regions of the tissue, suggesting asecretory pathway. Provided as reference, DAPI staining (blue) depictsnuclei and a GFAP antibody (red) depicts astrocytes. The AD patientdisplays much greater amount of soluble oligomers than the patient,which would be expected. The human brain extract and tissue slice datashow that the trimer affinity-purified antibodies can detect anddistinguish AD-related levels of soluble Aβ oligomers.

Trimer affinity-purified antibodies were also tested in hippocampalslices of Tg2576 AD transgenic mice. In Tg2576 mice, Aβ peptides arehighly expressed which leads to prolonged oligomer accumulation. FIG. 60depicts hippocampal slices of Tg2576 and wild-type mice at 6 months and12 months. Each slice was immunostained using the 6E10 antibodies (red)and the trimer affinity-purified antibodies (CL2A green). At 6 months,the Tg2576 mice display a high level of 6E10 signal and moderate levelof oligomer signal, suggesting a high accumulation of Aβ monomers andmoderate accumulation of Aβ oligomers. At 12 months, however, the trimeraffinity-purified antibodies exhibit much greater signal, which isconsistent with the continuous accumulation of oligomers as the miceage. Of note, the wild-type mice showed little to no signal for eitherantibody, as expected. These results suggest that the trimeraffinity-purified antibodies can detect the progression of AD inpatients and mice.

Triphenylmethane Dyes Bind Crosslinked Aβ Trimers

In this example, crystal violet, a triphenylmethane dye, is usedspecifically detect trimeric Aβ (FIG. D1). The dye is sized andpositioned to effectively bind within an Aβ trimer. While the precisemechanism of dye binding isn't precisely known, it is likely that thethree phenyl groups on crystal violet dye interact with the three F₂₀side chains through hydrophobic interactions. Additional proposedhydrophobic contacts include contacts between the methyl groups oncrystal violet and the three 131 side chains. Once the dye is bound, achange in absorbance is observe, possibly due to changes in polaritysurrounding the dye upon binding the trimer. Similarly, binding of thedye molecule increases fluorescence, likely due to the trimer/dyecomplex limiting vibrational modes of relaxation of the dye, favoringemission of photons. Accordingly, crystal violet can be used to measurethe relative concentration of Aβ trimer in solution using absorption orfluorescence spectra (See FIGS. 62A-63B).

In FIGS. 62A and 62B, absorbance of crystal violet with variousconcentrations of Aβ trimer is presented. As shown in FIG. 62A, crystalviolet in aqueous solution has a light violet color. As Aβ trimer isadded, the crystal violet molecules bind within the Aβ trimer, changingits absorbance from light violet to a blue. FIG. 62B depicts thisabsorbance change in a visible spectra chart. Crystal violet in solutionhas a peak absorbance around 540 nm. The peak absorbance of crystalviolet changes to around 600 nm when bound within an Aβ trimer.Accordingly, as the concentration of Aβ trimer is added to the crystalviolet solution, the absorbance at 600 nm increases (FIG. 62A).

FIGS. 63A and 63B provide fluorescence of crystal violet in solutionwith Aβ trimers. When crystal violet is bound to an Aβ trimer, it canemit light around 640 nm when stimulated (See pink band in FIG. 63A).Accordingly, as depicted in FIG. 63B, increases of Aβ trimerconcentration can be measured using crystal violet. As concentration ofAβ trimer increases, the amount of light emitted at 640 nm increases.

Synthesis of Synthetic Aβ Peptides

Described in the subsequent paragraphs are methods of synthesis ofsynthetic Aβ peptides. These methods are merely exemplary of how tosynthesize Aβ peptides. It should be understood that equivalent methodscan be performed to achieve Aβ peptides with similar desirableproperties.

Synthesis of Peptides

Loading of the resin. 2-Chlorotrityl chloride resin (300 mg, 1.2 mmol/g)was added to a Bio-Rad Poly-Prep chromatography column (10 mL). Theresin was suspended in dry CH₂Cl₂ (10 mL) and allowed to swell for 30min. The solution was drained from the resin and a solution ofBoc-Orn(Fmoc)-OH (0.50 equiv, 82 mg, 0.18 mmol) in 6% (v/v)2,4,6-collidine in dry CH₂Cl₂ (8 mL) was added immediately and thesuspension was gently agitated for 12 h. The solution was then drainedand a mixture of CH₂Cl₂/MeOH/N,N-diisopropylethylamine (DIPEA) (17:2:1,10 mL) was added immediately. The mixture was gently agitated for 1 h tocap the unreacted 2-chlorotrityl chloride resin sites. The resin wasthen washed with dry CH₂Cl₂ (2×) and dried by passing nitrogen throughthe vessel. This procedure typically yields 0.12-0.15 mmol of loadedresin (0.4-0.5 mmol/g loading).

Peptide Coupling.

The Boc-Orn(Fmoc)-2-chlorotrityl resin generated from the previous stepwas transferred to a microwave-assisted solid-phase peptide synthesizerreaction vessel and submitted to cycles of automated peptide couplingwith Fmoc-protected amino acid building blocks using a CEM Liberty 1Automated Microwave Peptide Synthesizer. The linear peptide wassynthesized from the C-terminus to the N-terminus. Each coupling cyclecomprised of Fmoc-deprotection with 20% (v/v) piperidine in DMF for 2min. at 50° C. (2×), washing with DMF (3×), coupling of the amino acid(0.75 mmol, 5 equiv) in the presence of HCTU (0.675 mmol, 4.5 equiv) and20% (v/v) N-methylmorpholine (NMM) in DMF for 10 min. at 50° C., andwashing with DMF (3×). Special coupling conditions were used for thephenylalanine that followed the N-methylphenylalanine: The phenylalaninewas double coupled (0.75 mmol, 5 equiv.) and allowed to react at ambienttemperature for 1 h per coupling with HATU (5 equiv) and HOAt (5 equiv)in 20% (v/v) NMM in DMF. After coupling of the last amino acid, theterminal Fmoc group was removed with 20% (v/v) piperidine in DMF (10min. 50° C.). The resin was transferred from the reaction vessel of thepeptide synthesizer to a Bio-Rad Poly-Prep chromatography column.

Cleavage of the Peptide from the Resin.

The linear peptide was cleaved from the resin by agitating the resin for1 h with a solution of 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) inCH₂Cl₂. (1:4, 7 mL). The suspension was filtered and the filtrate wascollected in a 250 mL round-bottomed flask. The resin was washed withadditional HFIP in CH₂Cl₂ (1:4, 7 mL) and then with CH₂Cl₂ (2×10 mL).The combined filtrates were concentrated by rotary evaporation to give awhite solid. The white solid was further dried by vacuum pump to affordthe crude protected linear peptide, which was macrolactamized withoutfurther purification.

Macrolactamization of the Linear Peptide.

The crude protected linear peptide was dissolved in dry DMF (150 mL).HOBt (114 mg, 0.75 mmol, 5 equiv) and HBTU (317 mg, 0.75 mmol, 5 equiv)were added to the solution. DIPEA (0.33 mL, 1.8 mmol, 12 equiv) wasadded to the solution and the mixture was stirred under nitrogen for 24h. The mixture was concentrated under reduced pressure to afford thecrude protected cyclic peptide.

Global Deprotection of the Cyclic Peptide.

The protected cyclic peptide was dissolved in TFA/triisopropylsilane(TIPS)/H₂O (18:1:1, 20 mL) in a 250 mL round-bottomed flask equippedwith a nitrogen-inlet adaptor. The solution was stirred for 1.5 h. Thereaction mixture was then concentrated by rotary evaporation underreduced pressure to afford the crude cyclic peptide as a thin yellowfilm on the side of the round-bottomed flask. The crude cyclic peptidewas immediately subjected to purification by reverse-phase HPLC(RP-HPLC), as described below.

Reverse-Phase HPLC Purification.

The peptide was dissolved in H₂O and acetonitrile (7:3, 10 mL), and thesolution was filtered through a 0.2 μm syringe filter and purified byRP-HPLC (gradient elution with 20-50% CH₃CN over 50 min). Pure fractionswere concentrated by rotary evaporation and lyophilized. Typicalsyntheses yielded ˜55 mg of either peptide as the TFA salt.

Synthesis of Crosslinked Trimers

Trimers were synthesized by oxidizing peptides in 20% aqueous DMSO. A 6mM solution of either lyophilized peptide was prepared gravimetricallyby dissolving the peptide in an appropriate amount of 20% (v/v) aqueousDMSO prepared with deionized water. The reaction was carried out in acapped 25-mL glass scintillation vial with rocking at room temperaturefor 48-72 h. Next, the reaction mixture was diluted to a concentrationof 300 μM peptide and transferred to a 500-mL round-bottomed flask. Thesolution was stirred with a magnetic stir bar for an additional 48 h.After 48 h, the reaction mixture was concentrated to ≤5 mL by rotaryevaporation and immediately subjected to RP-HPLC purification (gradientelution with 20-50% CH₃CN over 60 min). Pure fractions were concentratedby rotary evaporation and lyophilized. Typical syntheses yielded ˜10 mgtrimer 3 and ˜15 mg of trimer 4 from a 0.1 mmol scale synthesis ofpeptides 3 and 4.

Experimental Methods

Crystallization Procedure for Trimer 3

Trimer 3 afforded crystals in the same conditions that afforded crystalsof peptides 1 and 3-0.1 M HEPES buffer, and Jeffamine M-600. Theseconditions were further optimized accordingly to yield crystals oftrimer 4 suitable for X-ray crystallography. The optimized conditionsconsist of 0.1 M HEPES at pH 7.3 with 34% Jeffamine M-600.

Crystallization Procedure for Trimer 4.

Initial crystallization conditions for trimer 4 were determined usingthe hanging-drop vapor-diffusion method. Crystallization conditions werescreened using three crystallization kits in a 96-well plate format(Hampton Index, PEG/Ion, and Crystal Screen). Three 150 nL hanging dropsthat differed in the ratio of peptide to well solution were made percondition in each 96-well plate for a total of 864 experiments. Hangingdrops were made by combining an appropriate volume of trimer 4 (10 mg/mLin deionized water) with an appropriate volume of well solution tocreate three 150 nL hanging drops with 1:1, 1:2, and 2:1 peptide:wellsolution. The hanging drops were made using a TTP LabTech Mosquitonanodisperse instrument. Crystals of trimer 4 grew in ˜48 h in asolution of 0.1 M Tris buffer at pH 7.0 with 0.2 M MgCl₂ and 3.5 M1,6-hexanediol.

Crystallization conditions for trimer 4 were optimized using a 4×6matrix Hampton VDX 24-well plate. The Tris buffer pH was varied in eachrow in increments of 0.5 pH units (6.5, 7.0, 7.5, and 8.0) and the1,6-hexanediol concentration in each column in increments of 0.2 M (3.0M, 3.2 M, 3.4 M, 3.6 M, 3.8 M, 4.0 M). The first well in the 4×6 matrixwas prepared by combined 100 μL of 1 M Tris buffer at pH 6.5, 100 μL of2 M MgCl₂, 600 μL of 5 M 1,6-hexanediol, and 200 μL of deionized water.The other wells were prepared in analogous fashion, by combining 100 μLof Tris buffer of varying pH, 100 μL of 2 M MgCl₂, 5 M 1,6-hexanediol invarying amounts, and deionized water for a total volume of 1 mL in eachwell.

Three hanging-drops were prepared per borosilicate glass slide bycombining a solution of trimer 4 (10 mg/mL) and the well solution in thefollowing amounts: 1 μL:1 μL, 2 μL:1 μL, and 1 μL:2 μL. Slides wereinverted and pressed firmly against the silicone grease surrounding eachwell. Crystals of trimer 4 suitable for X-ray diffraction grew in ˜5days. Crystallization conditions were further optimized using smallervariations in Tris buffer pH (in increments of 0.25 pH units) and1,6-hexanediol concentrations (in increments of 0.1 M). Crystals wereharvested with a nylon loop attached to a copper or steel pin and flashfrozen in liquid nitrogen prior to data collection.

X-Ray Crystallographic Data Collection, Data Processing, and StructureDetermination for Trimers 3 and 4.

Diffraction data for trimers 3 and 4 were collected on a RigakuMicromax-007HF X-ray diffractometer with a rotating copper anode at 1.54Å wavelength with 0.5° oscillation. Diffraction data were collectedusing CrystalClear. Diffraction data were scaled and merged using XDS.Coordinates for the anomalous signals were determined by HySS in thePhenix software suite 1.10.1. Electron density maps were generated usinganomalous coordinates determined by HySS as initial positions inAutosol. Molecular manipulation of the model was performed with Coot.Coordinates were refined with phenix.refine.

Diffraction data for frillier 3 were also collected at the AdvancedLight Source at Lawrence Berkeley National Laboratory with a synchrotronsource at 1.00-Å wavelength to achieve higher resolution. Data fortrimer 3 suitable for refinement at 2.03 Å were obtained from thediffractometer; data for trimer 3 suitable for refinement at 1.90 Å wereobtained from the synchrotron. Diffraction data were scaled and mergedusing XDS. The electron density map was generated by molecularreplacement using the coordinates from the structure of trimer 3generated by soaking in KI using the Phaser in software suite Phenix1.10.1. Molecular manipulation of the model was performed with Coot.Coordinates were refined with phenix.refine.

Diffraction data for trimer 4 were also collected at the StanfordSynchrotron Radiation Lightsource (SSRL) with a synchrotron source at0.97-Å wavelength. Diffraction data were scaled and merged using XDS.The electron density map was generated by molecular replacement usingthe coordinates from the structure of trimer 4 generated by S-SAD usingthe Phaser in software suite Phenix 1.10.1. Molecular manipulation ofthe model was performed with Coot. Coordinates were refined withphenix.refine.

LDH Release and Caspase-3 Activation Assays.

The toxicities of peptides 1 and 3, and trimers 3 and 4 toward SH-SY5Ycells were assessed by LDH release and caspase-3 activation assays.Cells were incubated in the presence or absence of equivalentconcentrations of peptides 1 or 3, or trimers 3 and 4 for 72 h in96-well plates. The LDH release assay was performed using the Pierce LDHCytotoxicity Assay Kit from Thermo Scientific. The caspase-3 assay wasperformed using the Roche APO-One Homogeneous Caspase-3/7 Assay.Experiments were performed in replicates of five and an additional 10wells were used for controls. Cells were cultured in the inner 60 wells(rows B-G, columns 2-11) of the 96-well plate. DMEM:F12 media (100 μL)was added to the outer wells (rows A and H, columns 1 and 12), in orderto ensure the greatest reproducibility of data generated in the innerwells.

Preparation of Stock Solutions of Peptides 1 and 3, and Trimers 3 and 4.

A 10 mg/mL stock solution of peptides 1 or 3, or trimers 3 and 4 wasprepared gravimetrically by dissolving 1 mg of each compound in 100 μLof deionized water that was either filtered through a 0.2 μm syringefilter or autoclaved. The stock solution was used to create 180 μMworking solutions of peptides 1 or 3, or 60 μM working solutions oftrimers 3 and 4 (these solutions contain equivalent concentrations ofpeptide). The 180 μM working solutions of peptides 1 and 2 were seriallydiluted with deionized water to create 90 μM working solutions ofpeptides 1 and 2. The 60 μM working solutions of trimers 3 and 4 wereserially diluted with deionized water to create 30 μM, 15 μM, and 7.5 μMworking solutions of trimers 3 and 4.

Preparation of SH-SY5Y Cells for LDH Release and Caspase-3 Assays.

SH-SY5Y cells were plated in a 96-well plate at 30,000 cells per well.Cells were incubated in 100 μL of a 1:1 mixture of DMEM:F12 mediasupplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100μg/mL streptomycin at 37° C. in a 5% CO₂ atmosphere and allowed toadhere to the bottom of the plate for 24 hours.

Treatment of SH-SY5Y Cells with Peptides 1 and 2, and Trimers 3 and 4.

After 24 hours, the culture media was removed and replaced with 90 μL ofserum-free DMEM:F12 media. A 10 μL aliquot of the working solutions ofpeptides 1 or 2, or trimers 3 and 4 was added to each well, for awell-concentration of 18 μM and 9 μM for peptides 1 and 2, 6 μM and 3 μMfor trimer 3 or 6 μM, 3 μM, 1.5 μM, and 0.75 μM for trimer 4.Experiments were run in replicates of five. Five wells were used ascontrols and received a 10 μL aliquot of deionized water (vehicle).Another five wells were left untreated, to be subsequently used ascontrols with lysis buffer for the LDH release assay, or staurosporinefor the caspase-3 activation assay. Cells were incubated at 37° C. in a5% CO₂ atmosphere for 72 hours.

LDH Release Assay.

After 72 hours, 10 μL of 10× lysis buffer—included with the assaykit—was added to the five untreated wells, and the cells were incubatedfor an additional 45 minutes. After 45 min, a 50-μL aliquot of thesupernatant media from each well was transferred to a new 96-well plateand 50 μL of LDH substrate solution, prepared according tomanufacturer's protocol, was added to each well. The treated plates werestored in the dark for 30 min, then 100 μL of stop solution was added toeach well. The absorbance of each well was measured at 490 and 680 nm(A₄₀₀ and A₆₈₀). Data were processed by calculating the differentialabsorbance for each well (A₄₀₀-A₆₈₀) and comparing those values to thoseof the lysis buffer controls and the untreated controls: % celldeath=[(A₄₉₀−A₆₈₀)_(compound)−(A₄₉₀−A₆₈₀)_(vehicle)]/[(A₄₉₀−A₆₈₀)_(lysis)(A₄₉₀−A₆₈₀)_(vehicle)]

Caspase-3 Activation Assay.

After 67 hours, 10 μL of 10× staurosporine was added to the controlwells, and the cells were incubated for an additional 5 h. Next, thecompound-containing media was removed and replaced with 25 μL of freshserum-free DMEM/F12 media. A 25-μL aliquot of caspase-3 substrate,prepared according to manufacturer's protocol, was then added to eachwell. The plate was sealed with a clear adhesive plate sealer andfluorescence was monitored over 18 h while shaking at 250 rpm using aGemini XPS fluorescence plate reader (excitation at 499 nm, emission at521 nm). Data from the 18 h time point were processed by subtracting therelative fluorescence units (RFU) of the vehicle control wells from theRFU of the peptides 1 and 2 or trimers 3 and 4-treated wells.

Dot Blot Analysis of Peptides 1 and 2 and Trimers 3 and 4.

A 10 mg/mL stock solution of peptides 1 or 2, or trimers 3 or 4 wasprepared gravimetrically by dissolving 1 mg of each compound in 100 μLof deionized water that was either filtered through a 0.2 μm syringefilter. An aliquot of each stock solution was diluted with deionizedwater to make 3 mg/mL solutions. The 3 mg/mL solutions were thenserially diluted with deionized water to create 1.5 mg/mL, 0.75 mg/mL,and 0.37 mg/mL solutions. A 5 μL aliquot of each solution from theserial dilution was combined with 5 μL of a 2× solution of phosphatebuffered saline (PBS) at pH 7.4 to generate 1.5 mg/mL, 0.75 mg/mL, and0.37 mg/mL, and 0.18 mg/mL buffered solutions of peptides 1 or 2 ortrimers 3 or 4. A 1-μL aliquot of each buffered solution was spottedonto a nitrocellulose membrane and allowed to aft dry (˜5 min).Non-reactive sites were blocked with 10% (w/v) non-fat powdered milk inlow-Tween Tris-buffered saline (TBS-IT: 20 mM Tris, 137 mM NaCl; 0.01%Tween 20, pH 7.6) for 1 h at room temperature with rocking. The membranewas then incubated while rocking overnight at 4° C. in primary A11antibody (200 μg/mL) in 5% non-fat powdered milk in TBS-IT. The nextday, the membrane was washed with TBS-IT for 5 min (3×). The membranewas then incubated while rocking with horseradish peroxidase conjugatedgoat anti-rabbit antibody (100 μg/mL) (Jackson ImmunoResearch catalog#111-035-003) in 5% non-fat powdered milk in TBS-IT for 1 h at roomtemperature. The membrane was then washed with TBS-IT for 5 min (3×). A10 mL portion of chemiluminescence substrate (Thermo ScientificSuperSignal West Femto Maximum Sensitivity Substrate, product #34095)was prepared according to manufacturer's protocol and poured onto themembrane. The membrane was allowed to incubate in the chemiluminescencesubstrate for ˜10 min before imaging. The blot was imaged using astandard digital SLR camera.

Size Exclusion Chromatography.

The oligomerization of peptides 1 and 2 and trimers 3 and 4 was studiedby size-exclusion chromatography (SEC) at 4 CC in 50 mM sodiumacetate/50 mM acetic acid buffer (sodium acetate buffer) at pH 4.5 asfollows: Each peptide or trimer was dissolved in deionized water to aconcentration of 10 mg/mL. The peptide or trimer solutions were thendiluted to 1 mg/mL by adding 80 μL of the 10 mg/mL solutions to 720 μLof sodium acetate buffer. The peptide or trimer solutions were loadedonto a GE Superdex 75 10/300 GL column at 0.5 mL/min over 1 min. Afterloading, the samples were run with sodium acetate buffer at 1 mL/min,Chromatograms were recorded at 214 nm and normalized to the highestabsorbance value. Standards (cytochrome C, aprotinin, and vitamin B12)were run in the same fashion.

SDS-PAGE and Silver Staining.

The oligomerization of peptides 1 and 2 and trimers 3 and 4 was studiedby Tricine SDS-PAGE.

Sample Preparation.

Each peptide or trimer was dissolved in deionized water to aconcentration of 10 mg/mL. An aliquot of the 10 mg/mL solutions wasdiluted with deionized water to create 2 mg/mL solutions of peptides 1and 2, or 0.12 mg/mL solutions of trimers 3 and 4. The 1 mg/mL solutionsof peptides 1 and 2, as well as the 0.12 mg/mL solutions of trimers 3and 4 were further diluted with 2×SDS-PAGE loading buffer (100 mM Trisbuffer at pH 6.8, 20% (v/v) glycerol, and 4% SDS) to create 1 mg/mLworking solutions of peptides 1 and 2, and 0.06 mg/mL working solutionsof trimers 3 and 4. A 5 μL aliquot of each working solution was run on a16% polyacrylamide gel with a 4% stacking polyacrylamide gel. The gelswere run at a constant 60 volts at 4° C.

Staining with silver nitrate was used to visualize peptides 1 and 2 andtrimers 3 and 4 in the SDS-PAGE gel. Briefly, the gel was removed fromthe casting glass and rocked in fixing solution (50% (v/v) methanol and5% (v/v) acetic acid in deionized water) for 20 min. Next, the fixingsolution was discarded and the gel was rocked in 50% (v/v) methanol for10 min. Next, the 50% methanol was discarded and the gel was rocked indeionized water for 10 min. Next, the water was discarded and the gelwas rocked in 0.02% (w/v) sodium thiosulfate in deionized water for 1min. The sodium thiosulfate was discarded and the gel was rinsed withdeionized water (2×). After the last rinse, the gel was submerged inchilled 0.1% (w/v) silver nitrate in deionized water and rocked at 4° C.for 20 min. Next, the silver nitrate solution was discarded and the gelwas rinsed with deionized water (2×). To develop the gel, the gel wasincubated in developing solution (2% w/v sodium carbonate, 0.04%formaldehyde until the desired intensity of staining was reached (˜1-3min). When the desired intensity of staining was reached, thedevelopment was topped by discarding the developing solution andsubmerging the gel in 5% acetic acid.

Circular Dichroism Spectroscopy.

A 0.30 mg/mL solution of either trimer 3 or peptide 1 was prepared byadding 15 μL of 10 mg/mL stock solutions in deionized water to 385 μL of10 mM potassium phosphate buffer at pH 7.4. Each solution wastransferred to a 1 mm quartz cuvette for data acquisition. CD spectrawere acquired on a Masco J-810 circular dichroism spectropolarimeter atroom temperature. Data were collected using 0.2 nm intervals from 260 nmto 190 nm and averaged over five accumulations with smoothing.

TABLE 3 Sequencing Listing of Peptides Seq.  ID No. Name SequenceModifications  1 Aβ₁₋₄₀ DAEFRHDSGY EVHHQLKVFF AEDVGSNKGA IIGLMVGGVV  2Aβ₁₋₄₂ DAEFRHDSGY EVHHQLKVFF AEDVGSNKGA IIGLMVGGVV IA  3 FIG. 3AXCVFFCXXVG SNKGAIIGLX VX X₁ = Aβ₁₋₁₆, deleted; X₇ = E, Q, K; X₈ = D,N;X₂₀ = M, Orn, MetO; X₂₂ = Aβ₃₇₋₄₀, Aβ₃₇₋₄₂, deleted;Optional N-substitution on F₅ and G₁₈  (Me, alkyl, aryl, etc.)  4FIG. 3B XLVFFAXXVG SNKGCIIGCX VXX₁ = Aβ₁₋₁₆, deleted; X₇ = E, Q, K; X₈ = D,N;X₂₀ = M, Orn, MetO; X₂₂ = Aβ₃₇₋₄₀, Aβ₃₇₋₄₂, deleted;Optional N-substitution on F₅ and G₁₈  (Me, alkyl, aryl, etc.)  5FIG. 4A XCVFFCXX X₁ = Orn; X₇ = E, Q, K; X₈ = D, N; TopOption N-substitution of F₅ (Me, alkyl, aryl, etc.)  6 FIG. 4A XAIIGLXVX₁ = Orn; X₇ = M, Orn, MetO; BottomOption N-substitution of G₅ (Me, alkyl, aryl, etc.)  7 FIG. 4B XLVFFAXXX₁ = Orn; X₇ = E, Q, K; X₈ = D, N; TopOption N-substitution of F₅ (Me, alkyl, aryl, etc.)  8 FIG. 4B XCIIGCXVX₁ = Orn; X₇ = M, Orn, MetO; BottomOption N-substitution of G₅ (Me, alkyl, aryl, etc.)  9 Aβ₁₋₁₆DAEFRHDSGY EVHHQK 10 Aβ₃₇₋₄₀ GGVV 11 Aβ₃₇₋₄₂ GGVVIA 12 FIG. 12 XLVFFAXXX₁ = Orn; X₇ = E, Q, K; X₈ = D, N; TopOption N-substitution of F₅ (Me, alkyl, aryl, etc.) 13 FIG. 12 XAIGGLXVX₁ = Orn; X₇ = M, Orn, MetO; BottomOption N-substitution of G₅ (Me, alkyl, aryl, etc.) 14 FIG. 12XLVFFAXXVG SNKGAIIGLX VX X₁ = Aβ₁₋₁₆, deleted; X₇ = E, Q, K; X₈ = D,N;full X₂₀ = M, Orn, MetO; X₂₂ = Aβ₃₇₋₄₀, Aβ₃₇₋₄₂, deleted;Optional N-substitution on F₅ and G₁₈  (Me, alkyl, aryl, etc.) 15FIG. 13 XKLVFFAX X₁ = Orn; X₇ = E, Q, K; X₈ = D, N; TopOption N-substitution of F₅ (Me, alkyl, aryl, etc.) 16 FIG. 13 XAIIGLXVX₁ = Orn; X₇ = M, Orn, MetO; BottomOption N-substitution of G₅ (Me, alkyl, aryl, etc.) 17 FIG. 13XKLVFFAXXV GSNKGAIIGL X₁ =Aβ₁₋₁₆, deleted; X₈ = E, Q, K; X₉ = D,N; fullXVX X₂₁ = M, Orn, MetO; X₂₃ = Aβ₃₇₋₄₀, Aβ₃₇₋₄₂, deleted;Optional N-substitution on F₅ and G₁₉  (Me, alkyl, aryl, etc.) 18Peptide XLVFFAED X₁ = Orn 1 Top 19 Peptide XAIIGLXVX₁ = Orn; X₇ = Orn; N-methylation on G₅ 1 Bottom 20 Peptide XLVFFAEDX₁ = Orn; N-methylation of F₅ 2 Top 21 Peptide XAIIGLXVX₁ = Orn; X₇ = Orn 2 Bottom 22 Peptide XCVFFCED X₁ = Orn 3 Top 23Peptide XAIIGLXV X₁ = Orn; X₇ = Orn; N-methylation on G₅ 3 Bottom 24Peptide XCVFFCED X₁ = Orn; N-methylation of F₅ 4 Top 25 Peptide XAIIGLXVX₁ = Orn; X₇ = Orn 4 Bottom 26 Peptide XLVFFAEDX₁ = Orn; F₄ = para-iodophenylalanine 5 Top 27 Peptide XAIIGLMVX₁ = Orn; N-methylation of G₅ 5 Bottom 28 Peptide XKLVFFAEX₁ = Orn; F₅ = para-iodophenylalanine 6 Top 29 Peptide XAIIGLMVX₁ = Orn; N-methylation of G₅ 6 Bottom 30 Peptide XQKLVFFAX₁ = Orn; F₆ = para-iodophenylalanine 7 Top 31 Peptide XAIIGLMVX₁ = Orn; N-methylation of G₅ 7 Bottom 32 Aβ₁₇₋₃₆ LVFFAEDVGS NKGAIIGLMV33 peptide XKLVFFAE X₁ = Orn; N-methylation of F₅ 8 top 34 peptideXAIIGLMV X₁ = Orn 8 bottom 35 Aβ616₋₃₆ KVLFFAEDVG SNKGAIIGLM V 36peptide XKLVFFAE X₁ = Orn; N-methylation of F₅ 9 top 37 peptide XAIIGLMVX₁ = Orn; N-methylation of G₅ 9 bottom 38 peptide XKVFFAADX₁ = Orn; N-methylation of F₅ 10 top 39 peptide XAIIGLMV X₁ = Orn10 bottom

DOCTRINE OF EQUIVALENTS

Those skilled in the art will appreciate that the foregoing examples anddescriptions of various preferred embodiments of the present inventionare merely illustrative of the invention as a whole, and that variationsin the steps and various components of the present invention may be madewithin the spirit and scope of the invention. Accordingly, the presentinvention is not limited to the specific embodiments described hereinbut, rather, is defined by the scope of the appended claims.

What is claimed is:
 1. A method of producing antibodies having affinityfor soluble beta-amyloid oligomers comprising: administering to animmunocompetent animal with an immunogenic cocktail comprising asynthetic beta-amyloid trimer; wherein the beta-amyloid trimer is atrimer selected from the group consisting of: a trimer having a first, asecond, and a third synthetic beta-amyloid peptide, each peptidecomprises Seq. ID No. 3 or a substantially similar sequence; wherein thecysteine in amino acid position two of the first peptide forms adisulfide linkage with the cysteine in amino acid position six of thesecond peptide; wherein the cysteine in amino acid position two of thesecond peptide forms a disulfide linkage with the cysteine in amino acidposition six of the third peptide; wherein the cysteine in amino acidposition two of the third peptide forms a disulfide linkage with thecysteine in amino acid position six of the first peptide; and whereinthe substantially similar sequence consists of an addition, a removal,or a substitution of up to three amino acids yet maintains each cysteineamino acid of the peptide in its identified position; a trimer having afirst, a second, and a third synthetic beta-amyloid peptide, eachpeptide comprises Seq. ID No. 4 or a substantially similar sequence;wherein the cysteine in amino acid position fifteen of the first peptideforms a disulfide linkage with the cysteine in amino acid positionnineteen of the second peptide; wherein the cysteine in amino acidposition fifteen of the second peptide forms a disulfide linkage withthe cysteine in amino acid position nineteen of the third peptide;wherein the cysteine in amino acid position fifteen of the third peptideforms a disulfide linkage with the cysteine in amino acid positionnineteen of the first peptide; and wherein the substantially similarsequence consists of an addition, a removal, or a substitution of up tothree amino acids yet maintains each cysteine amino acid of the peptidein its identified position; a trimer having a first, a second, and athird synthetic beta-amyloid peptide, each peptide consists of a firstand a second strand, the first strand comprises Seq. ID No. 5 or asubstantially similar sequence, and the second strand comprises Seq. IDNo. 6 or a substantially similar sequence; wherein the first and secondstrand are covalently linked by the delta-amino group of the side chainof the N-terminal ornithine of the first strand to the C-terminus of thesecond strand, and wherein the first and second strand are alsocovalently linked by the delta-amino group of the side chain of theN-terminal ornithine of the second strand to the C-terminus of the firststrand; wherein the cysteine in amino acid position two of the firststrand of the first peptide forms a disulfide linkage with the cysteinein amino acid position six of the first strand of the second peptide;wherein the cysteine in amino acid position two of the first strand ofthe second peptide forms a disulfide linkage with the cysteine in aminoacid position six of the first strand of the third peptide; wherein thecysteine in amino acid position two of the first strand of the thirdpeptide forms a disulfide linkage with the cysteine in amino acidposition six of the first strand of the first peptide; and wherein anyof the substantially similar sequences is a sequence that allowsconsists of an addition, a removal, or a substitution of up to threeamino acids yet maintains each cysteine amino acid of the peptide itsidentified position; and a trimer having a first, a second, and a thirdsynthetic beta-amyloid peptide, each peptide consists of a first and asecond strand, the first strand comprises Seq. ID No. 7 or asubstantially similar sequence, and the second strand comprises Seq. IDNo. 8 or a substantially similar sequence; wherein the first and secondstrand are covalently linked by the delta-amino group of the side chainof the N-terminal ornithine of the first strand to the C-terminus of thesecond strand, and wherein the first and second strand are alsocovalently linked by the delta-amino group of the side chain of theN-terminal ornithine of the second strand to the C-terminus of the firststrand; wherein the cysteine in amino acid position two of the secondstrand of the first peptide forms a disulfide linkage with the cysteinein amino acid position six of the second strand of the second peptide;wherein the cysteine in amino acid position two of the second strand ofthe second peptide forms a disulfide linkage with the cysteine in aminoacid position six of the second strand of the third peptide; wherein thecysteine in amino acid position two of the second strand of the thirdpeptide forms a disulfide linkage with the cysteine in amino acidposition six of the second strand of the first peptide; and wherein anyof the substantially similar sequences is a sequence that allowsconsists of an addition, a removal, or a substitution of up to threeamino acids yet maintains each cysteine amino acid of the peptide in itsidentified position.
 2. The method of claim 1, wherein at least onesynthetic beta-amyloid peptide incorporates an ornithine in the aminoacid position that corresponds to methionine35 of a naturally occurringbeta-amyloid peptide.
 3. The method of claim 1, wherein at least onecentral amino acid is N-methylated.
 4. The method of claim 1, whereinthe synthetic beta-amyloid peptide has at least one amino acid mutationthat corresponds to familial Alzheimer's disease.
 5. The method of claim1, wherein any of the substantially similar sequences is a sequence thatallows consists of an addition, a removal, or a substitution of up totwo amino acids but still maintains each cysteine amino acid of thepeptide in its identified position.
 6. The method of claim 1, whereinany of the substantially similar sequences is a sequence that allowsconsists of an addition, a removal, or a substitution of one amino acidsbut still maintains each cysteine amino acid of the peptide in itsidentified position.
 7. The method of claim 1, wherein any of thesubstantially similar sequences is an identical sequence that does nothave an addition, a removal, or a substitution of an amino acid.
 8. Themethod of claim 1 further comprising: harvesting antibodies from theimmunocompetent animal.
 9. The method of producing antibodies of claim 1further comprising repeating administration of beta-amyloid trimers tothe immunocompetent animal.
 10. The method of claim 1, wherein theimmunocompetent animal is selected from the group consisting of human,rabbit, goat, mouse, rat, chicken, and guinea pig.
 11. The method ofclaim 1, wherein the immunogenic cocktail further comprises an adjuvant.12. The method of claim 1, wherein the adjuvant is Freund's adjuvant.13. The method of claim 1, wherein the at least one beta-amyloid trimeris conjugated with hemocyanin.
 14. The method of claim 1, wherein theimmunocompetent animal is a human individual for the purpose ofvaccination.